w4mcorcov: w4mcorcov_calc.R annotate

annotate w4mcorcov_calc.R @ 2:a06344808ffc draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99

author	eschen42
date	Sat, 11 Nov 2017 00:08:20 -0500
parents	e25fd8a13665
children	61935618f92c

rev	line source
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	1 # center with 'colMeans()' - ref: http://gastonsanchez.com/visually-enforced/how-to/2014/01/15/Center-data-in-R/
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	2 center_colmeans <- function(x) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	3 xcenter = colMeans(x)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	4 x - rep(xcenter, rep.int(nrow(x), ncol(x)))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	5 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	6
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	7 #### OPLS-DA
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	8 algoC <- "nipals"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	9
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	10 do_detail_plot <- function(x_dataMatrix, x_predictor, x_is_match, x_algorithm, x_prefix, x_show_labels, x_show_loado_labels, x_progress = print, x_env) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	11 off <- function(x) if (x_show_labels == "0") 0 else x
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	12 if (x_is_match && ncol(x_dataMatrix) > 0 && length(unique(x_predictor))> 1) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	13 my_oplsda <- opls(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	14 x = x_dataMatrix
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	15 , y = x_predictor
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	16 , algoC = x_algorithm
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	17 , predI = 1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	18 , orthoI = if (ncol(x_dataMatrix) > 1) 1 else 0
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	19 , printL = FALSE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	20 , plotL = FALSE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	21 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	22 my_oplsda_suppLs_y_levels <- levels(as.factor(my_oplsda@suppLs$y))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	23 fctr_lvl_1 <- my_oplsda_suppLs_y_levels[1]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	24 fctr_lvl_2 <- my_oplsda_suppLs_y_levels[2]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	25 my_cor_vs_cov <- cor_vs_cov(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	26 matrix_x = x_dataMatrix
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	27 , ropls_x = my_oplsda
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	28 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	29 with(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	30 my_cor_vs_cov
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	31 , {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	32 min_x <- min(covariance)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	33 max_x <- max(covariance)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	34 lim_x <- max(sapply(X=c(min_x, max_x), FUN=abs))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	35 covariance <- covariance / lim_x
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	36 lim_x <- 1.2
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	37 main_label <- sprintf("%s for levels %s versus %s", x_prefix, fctr_lvl_1, fctr_lvl_2)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	38 main_cex <- min(1.0, 46.0/nchar(main_label))
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	39 # "It is generally accepted that a variable should be selected if vj>1, [27–29],
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	40 # but a proper threshold between 0.83 and 1.21 can yield more relevant variables according to [28]."
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	41 # (Mehmood 2012 doi:10.1186/1748-7188-6-27)
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	42 vipco <- pmax(0, pmin(1,(vip4p-0.83)/(1.21-0.83)))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	43 alpha <- 0.1 + 0.4 * vipco
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	44 red <- as.numeric(correlation > 0) * vipco
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	45 blue <- as.numeric(correlation < 0) * vipco
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	46 plus_cor <- correlation
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	47 plus_cov <- covariance
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	48 cex <- 0.75
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	49 plot(
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	50 y = plus_cor
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	51 , x = plus_cov
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	52 , type="p"
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	53 , xlim=c(-lim_x, lim_x + off(0.2))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	54 , ylim=c(-1.0 - off(0.2), 1.0)
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	55 , xlab = sprintf("relative covariance(feature,t1)")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	56 , ylab = sprintf("correlation(feature,t1)")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	57 , main = main_label
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	58 , cex.main = main_cex
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	59 , cex = cex
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	60 , pch = 16
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	61 , col = rgb(blue = blue, red = red, green = 0, alpha = alpha)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	62 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	63 low_x <- -0.7 * lim_x
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	64 high_x <- 0.7 * lim_x
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	65 text(x = low_x, y = -0.05, labels = fctr_lvl_1, col = "blue")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	66 text(x = high_x, y = 0.05, labels = fctr_lvl_2, col = "red")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	67 if ( x_show_labels != "0" ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	68 my_loadp <- loadp
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	69 my_loado <- loado
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	70 names(my_loadp) <- tsv1$featureID
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	71 names(my_loado) <- tsv1$featureID
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	72 if ( x_show_labels == "ALL" ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	73 n_labels <- length(loadp)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	74 } else {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	75 n_labels <- as.numeric(x_show_labels)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	76 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	77 n_labels <- min( n_labels, (1 + length(loadp)) / 2 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	78 labels_to_show <- c(
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	79 names(head(sort(my_loadp),n = n_labels))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	80 , names(tail(sort(my_loadp),n = n_labels))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	81 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	82 if ( x_show_loado_labels ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	83 labels_to_show <- c(
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	84 labels_to_show
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	85 , names(head(sort(my_loado),n = n_labels))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	86 , names(tail(sort(my_loado),n = n_labels))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	87 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	88 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	89 labels <- unname(sapply( X = tsv1$featureID, FUN = function(x) if( x %in% labels_to_show ) x else "" ))
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	90 text(
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	91 y = plus_cor - 0.013
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	92 , x = plus_cov + 0.020
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	93 , cex = 0.3
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	94 , labels = labels
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	95 , col = rgb(blue = blue, red = red, green = 0, alpha = 0.2 + 0.8 * alpha)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	96 , srt = -30 # slant 30 degrees downward
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	97 , adj = 0 # left-justified
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	98 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	99 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	100 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	101 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	102 typeVc <- c("correlation", # 1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	103 "outlier", # 2
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	104 "overview", # 3
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	105 "permutation", # 4
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	106 "predict-train", # 5
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	107 "predict-test", # 6
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	108 "summary", # 7 = c(2,3,4,9)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	109 "x-loading", # 8
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	110 "x-score", # 9
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	111 "x-variance", # 10
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	112 "xy-score", # 11
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	113 "xy-weight" # 12
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	114 ) # [c(3,8,9)] # [c(4,3,8,9)]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	115 if ( length(my_oplsda@orthoVipVn) > 0 ) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	116 my_typevc <- typeVc[c(9,3,8)]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	117 } else {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	118 my_typevc <- c("(dummy)","overview","(dummy)")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	119 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	120 for (my_type in my_typevc) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	121 if (my_type %in% typeVc) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	122 # print(sprintf("plotting type %s", my_type))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	123 plot(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	124 x = my_oplsda
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	125 , typeVc = my_type
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	126 , parCexN = 0.4
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	127 , parDevNewL = FALSE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	128 , parLayL = TRUE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	129 , parEllipsesL = TRUE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	130 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	131 } else {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	132 # print("plotting dummy graph")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	133 plot(x=1, y=1, xaxt="n", yaxt="n", xlab="", ylab="", type="n")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	134 text(x=1, y=1, labels="no orthogonal projection is possible")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	135 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	136 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	137 return (my_cor_vs_cov)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	138 } else {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	139 # x_progress(sprintf("x_is_match = %s, ncol(x_dataMatrix) = %d, length(unique(x_predictor)) = %d",x_is_match, ncol(x_dataMatrix), length(unique(x_predictor))))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	140 return (NULL)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	141 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	142 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	143
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	144 # S-PLOT and OPLS reference: Wiklund_2008 doi:10.1021/ac0713510
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	145 corcov_calc <- function(calc_env, failure_action = stop, progress_action = function(x){}, corcov_tsv_action = function(t){}, salience_tsv_action = function(t){}) {
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	146 if ( ! is.environment(calc_env) ) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	147 failure_action("corcov_calc: fatal error - 'calc_env' is not an environment")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	148 return ( FALSE )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	149 }
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	150 if ( ! is.function(corcov_tsv_action) ) {
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	151 failure_action("corcov_calc: fatal error - 'corcov_tsv_action' is not a function")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	152 return ( FALSE )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	153 }
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	154 if ( ! is.function(salience_tsv_action) ) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	155 failure_action("salience_calc: fatal error - 'salience_tsv_action' is not a function")
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	156 return ( FALSE )
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	157 }
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	158
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	159 # extract parameters from the environment
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	160 vrbl_metadata <- calc_env$vrbl_metadata
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	161 vrbl_metadata_names <- vrbl_metadata[,1]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	162 smpl_metadata <- calc_env$smpl_metadata
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	163 data_matrix <- calc_env$data_matrix
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	164 pairSigFeatOnly <- calc_env$pairSigFeatOnly
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	165 facC <- calc_env$facC
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	166 tesC <- calc_env$tesC
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	167 # extract the levels from the environment
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	168 originalLevCSV <- levCSV <- calc_env$levCSV
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	169 # matchingC is one of { "none", "wildcard", "regex" }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	170 matchingC <- calc_env$matchingC
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	171 labelFeatures <- calc_env$labelFeatures
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	172 labelOrthoFeatures <- calc_env$labelOrthoFeatures
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	173
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	174 # arg/env checking
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	175 if (!(facC %in% names(smpl_metadata))) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	176 failure_action(sprintf("bad parameter! Factor name '%s' not found in sampleMetadata", facC))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	177 return ( FALSE )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	178 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	179
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	180 mz <- vrbl_metadata$mz
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	181 names(mz) <- vrbl_metadata$variableMetadata
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	182 mz_lookup <- function(feature) unname(mz[feature])
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	183
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	184 rt <- vrbl_metadata$rt
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	185 names(rt) <- vrbl_metadata$variableMetadata
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	186 rt_lookup <- function(feature) unname(rt[feature])
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	187
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	188 # calculate salience_df as data.frame(feature, max_level, max_median, max_rcv, mean_median, salience, salient_rcv)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	189 salience_df <- calc_env$salience_df <- w4msalience(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	190 data_matrix = data_matrix
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	191 , sample_class = smpl_metadata[,facC]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	192 , failure_action = failure_action
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	193 )
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	194 salience_tsv_action({
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	195 my_df <- data.frame(
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	196 featureID = salience_df$feature
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	197 , salientLevel = salience_df$max_level
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	198 , salientRCV = salience_df$salient_rcv
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	199 , salience = salience_df$salience
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	200 , mz = mz_lookup(salience_df$feature)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	201 , rt = rt_lookup(salience_df$feature)
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	202 )
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	203 my_df[order(-my_df$salience),]
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	204 })
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	205
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	206 # transform wildcards to regexen
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	207 if (matchingC == "wildcard") {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	208 # strsplit(x = "hello,wild,world", split = ",")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	209 levCSV <- gsub("[.]", "[.]", levCSV)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	210 levCSV <- strsplit(x = levCSV, split = ",")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	211 levCSV <- sapply(levCSV, utils::glob2rx, trim.tail = FALSE)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	212 levCSV <- paste(levCSV, collapse = ",")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	213 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	214 # function to determine whether level is a member of levCSV
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	215 isLevelSelected <- function(lvl) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	216 matchFun <- if (matchingC != "none") grepl else `==`
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	217 return(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	218 Reduce(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	219 f = "\|\|"
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	220 , x = sapply(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	221 X = strsplit(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	222 x = levCSV
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	223 , split = ","
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	224 , fixed = TRUE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	225 )[[1]]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	226 , FUN = matchFun
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	227 , lvl
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	228 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	229 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	230 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	231 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	232
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	233 # transpose matrix because ropls matrix is the transpose of XCMS matrix
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	234 # Wiklund_2008 centers and pareto-scales data before OPLS-DA S-plot
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	235 # center
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	236 cdm <- center_colmeans(t(data_matrix))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	237 # pareto-scale
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	238 my_scale <- sqrt(apply(cdm, 2, sd, na.rm=TRUE))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	239 scdm <- sweep(cdm, 2, my_scale, "/")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	240
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	241 # pattern to match column names like k10_kruskal_k4.k3_sig
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	242 col_pattern <- sprintf('^%s_%s_(.)[.](.)_sig$', facC, tesC)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	243 # column name like k10_kruskal_sig
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	244 intersample_sig_col <- sprintf('%s_%s_sig', facC, tesC)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	245 # get the facC column from sampleMetadata, dropping to one dimension
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	246 smpl_metadata_facC <- smpl_metadata[,facC]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	247
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	248 # allocate a slot in the environment for the contrast_list, each element of which will be a data.frame with this structure:
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	249 # - feature ID
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	250 # - value1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	251 # - value2
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	252 # - Wiklund_2008 correlation
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	253 # - Wiklund_2008 covariance
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	254 # - Wiklund_2008 VIP
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	255 calc_env$contrast_list <- list()
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	256
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	257
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	258 did_plot <- FALSE
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	259 if (tesC != "none") {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	260 # for each column name, extract the parts of the name matched by 'col_pattern', if any
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	261 the_colnames <- colnames(vrbl_metadata)
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	262 if ( ! Reduce( f = "\|\|", x = grepl(tesC, the_colnames) ) ) {
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	263 failure_action(sprintf("bad parameter! variableMetadata must contain results of W4M Univariate test '%s'.", tesC))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	264 return ( FALSE )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	265 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	266 col_matches <- lapply(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	267 X = the_colnames,
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	268 FUN = function(x) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	269 regmatches( x, regexec(col_pattern, x) )[[1]]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	270 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	271 )
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	272 ## first contrast each selected level with all other levels combined into one "super-level" ##
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	273 # process columns matching the pattern
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	274 level_union <- c()
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	275 for (i in 1:length(col_matches)) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	276 col_match <- col_matches[[i]]
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	277 if (length(col_match) > 0) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	278 # it's an actual match; extract the pieces, e.g., k10_kruskal_k4.k3_sig
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	279 vrbl_metadata_col <- col_match[1] # ^^^^^^^^^^^^^^^^^^^^^ # Column name
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	280 fctr_lvl_1 <- col_match[2] # ^^ # Factor-level 1
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	281 fctr_lvl_2 <- col_match[3] # ^^ # Factor-level 2
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	282 # only process this column if both factors are members of lvlCSV
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	283 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	284 if (is_match) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	285 level_union <- c(level_union, col_match[2], col_match[3])
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	286 }
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	287 }
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	288 }
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	289 level_union <- unique(sort(level_union))
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	290 overall_significant <- 1 == ( if (intersample_sig_col %in% colnames(vrbl_metadata)) vrbl_metadata[,intersample_sig_col] else TRUE )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	291 if ( length(level_union) > 2 ) {
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	292 chosen_samples <- smpl_metadata_facC %in% level_union
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	293 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	294 col_selector <- vrbl_metadata_names[ overall_significant ]
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	295 my_matrix <- scdm[ chosen_samples, col_selector, drop = FALSE ]
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	296 plot_action <- function(fctr_lvl_1, fctr_lvl_2) {
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	297 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", fctr_lvl_1, fctr_lvl_2))
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	298 predictor <- sapply( X = chosen_facC, FUN = function(fac) if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2 )
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	299 my_cor_cov <- do_detail_plot(
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	300 x_dataMatrix = my_matrix
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	301 , x_predictor = predictor
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	302 , x_is_match = is_match
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	303 , x_algorithm = algoC
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	304 , x_prefix = if (pairSigFeatOnly) "Significantly contrasting features" else "Significant features"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	305 , x_show_labels = labelFeatures
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	306 , x_show_loado_labels = labelOrthoFeatures
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	307 , x_progress = progress_action
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	308 , x_env = calc_env
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	309 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	310 if ( is.null(my_cor_cov) ) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	311 progress_action("NOTHING TO PLOT.")
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	312 } else {
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	313 my_tsv <- my_cor_cov$tsv1
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	314 my_tsv$mz <- mz_lookup(my_tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	315 my_tsv$rt <- rt_lookup(my_tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	316 my_tsv["level1Level2Sig"] <- vrbl_metadata[ match(my_tsv$featureID, vrbl_metadata_names), vrbl_metadata_col ]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	317 tsv <<- my_tsv
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	318 corcov_tsv_action(tsv)
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	319 did_plot <<- TRUE
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	320 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	321 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	322 if ( length(level_union) != 2 ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	323 fctr_lvl_2 <- "other"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	324 for ( fctr_lvl_1 in level_union[1:length(level_union)] ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	325 plot_action(fctr_lvl_1, fctr_lvl_2)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	326 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	327 } else {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	328 plot_action(fctr_lvl_1 = level_union[1], fctr_lvl_2 = level_union[2])
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	329 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	330 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	331
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	332 if ( length(level_union) > 1 ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	333 ## next, contrast each selected level with each of the other levels individually ##
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	334 # process columns matching the pattern
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	335 for (i in 1:length(col_matches)) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	336 # for each potential match of the pattern
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	337 col_match <- col_matches[[i]]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	338 if (length(col_match) > 0) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	339 # it's an actual match; extract the pieces, e.g., k10_kruskal_k4.k3_sig
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	340 vrbl_metadata_col <- col_match[1] # ^^^^^^^^^^^^^^^^^^^^^ # Column name
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	341 fctr_lvl_1 <- col_match[2] # ^^ # Factor-level 1
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	342 fctr_lvl_2 <- col_match[3] # ^^ # Factor-level 2
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	343 # only process this column if both factors are members of lvlCSV
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	344 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	345 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", fctr_lvl_1, fctr_lvl_2))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	346 # TODO delete next line displaying currently-processed column
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	347 # cat(sprintf("%s %s %s %s\n", vrbl_metadata_col, fctr_lvl_1, fctr_lvl_2, is_match))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	348 # choose only samples with one of the two factors for this column
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	349 chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	350 predictor <- smpl_metadata_facC[chosen_samples]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	351 # extract only the significantly-varying features and the chosen samples
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	352 fully_significant <- 1 == vrbl_metadata[,vrbl_metadata_col] * ( if (intersample_sig_col %in% colnames(vrbl_metadata)) vrbl_metadata[,intersample_sig_col] else TRUE )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	353 col_selector <- vrbl_metadata_names[ if ( pairSigFeatOnly ) fully_significant else overall_significant ]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	354 my_matrix <- scdm[ chosen_samples, col_selector, drop = FALSE ]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	355 my_cor_cov <- do_detail_plot(
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	356 x_dataMatrix = my_matrix
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	357 , x_predictor = predictor
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	358 , x_is_match = is_match
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	359 , x_algorithm = algoC
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	360 , x_prefix = if (pairSigFeatOnly) "Significantly contrasting features" else "Significant features"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	361 , x_show_labels = labelFeatures
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	362 , x_show_loado_labels = labelOrthoFeatures
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	363 , x_progress = progress_action
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	364 , x_env = calc_env
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	365 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	366 if ( is.null(my_cor_cov) ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	367 progress_action("NOTHING TO PLOT.")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	368 } else {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	369 tsv <- my_cor_cov$tsv1
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	370 tsv$mz <- mz_lookup(tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	371 tsv$rt <- rt_lookup(tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	372 tsv["level1Level2Sig"] <- vrbl_metadata[ match(tsv$featureID, vrbl_metadata_names), vrbl_metadata_col ]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	373 corcov_tsv_action(tsv)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	374 did_plot <- TRUE
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	375 }
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	376 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	377 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	378 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	379 } else { # tesC == "none"
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	380 level_union <- unique(sort(smpl_metadata_facC))
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	381 if ( length(level_union) > 1 ) {
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	382 if ( length(level_union) > 2 ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	383 ## pass 1 - contrast each selected level with all other levels combined into one "super-level" ##
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	384 completed <- c()
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	385 lapply(
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	386 X = level_union
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	387 , FUN = function(x) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	388 fctr_lvl_1 <- x[1]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	389 fctr_lvl_2 <- {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	390 if ( fctr_lvl_1 %in% completed )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	391 return("DUMMY")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	392 # strF(completed)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	393 completed <<- c(completed, fctr_lvl_1)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	394 setdiff(level_union, fctr_lvl_1)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	395 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	396 chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	397 fctr_lvl_2 <- "other"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	398 # print( sprintf("sum(chosen_samples) %d, factor_level_2 %s", sum(chosen_samples), fctr_lvl_2) )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	399 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", fctr_lvl_1, fctr_lvl_2))
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	400 if (length(unique(chosen_samples)) < 1) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	401 progress_action("NOTHING TO PLOT...")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	402 } else {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	403 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	404 predictor <- sapply( X = chosen_facC, FUN = function(fac) if ( fac == fctr_lvl_1 ) fctr_lvl_1 else fctr_lvl_2 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	405 my_matrix <- scdm[ chosen_samples, , drop = FALSE ]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	406 # only process this column if both factors are members of lvlCSV
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	407 is_match <- isLevelSelected(fctr_lvl_1)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	408 my_cor_cov <- do_detail_plot(
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	409 x_dataMatrix = my_matrix
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	410 , x_predictor = predictor
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	411 , x_is_match = is_match
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	412 , x_algorithm = algoC
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	413 , x_prefix = "Features"
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	414 , x_show_labels = labelFeatures
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	415 , x_show_loado_labels = labelOrthoFeatures
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	416 , x_progress = progress_action
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	417 , x_env = calc_env
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	418 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	419 if ( is.null(my_cor_cov) ) {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	420 progress_action("NOTHING TO PLOT")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	421 } else {
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	422 tsv <- my_cor_cov$tsv1
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	423 tsv$mz <- mz_lookup(tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	424 tsv$rt <- rt_lookup(tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	425 corcov_tsv_action(tsv)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	426 did_plot <<- TRUE
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	427 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	428 }
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	429 #print("baz")
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	430 "dummy" # need to return a value; otherwise combn fails with an error
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	431 }
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	432 )
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	433 }
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	434 ## pass 2 - contrast each selected level with each of the other levels individually ##
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	435 completed <- c()
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	436 utils::combn(
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	437 x = level_union
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	438 , m = 2
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	439 , FUN = function(x) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	440 fctr_lvl_1 <- x[1]
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	441 fctr_lvl_2 <- x[2]
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	442 chosen_samples <- smpl_metadata_facC %in% c(fctr_lvl_1, fctr_lvl_2)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	443 # print( sprintf("sum(chosen_samples) %d, factor_level_2 %s", sum(chosen_samples), fctr_lvl_2) )
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	444 progress_action(sprintf("calculating/plotting contrast of %s vs. %s", fctr_lvl_1, fctr_lvl_2))
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	445 if (length(unique(chosen_samples)) < 1) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	446 progress_action("NOTHING TO PLOT...")
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	447 } else {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	448 chosen_facC <- as.character(smpl_metadata_facC[chosen_samples])
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	449 predictor <- chosen_facC
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	450 my_matrix <- scdm[ chosen_samples, , drop = FALSE ]
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	451 # only process this column if both factors are members of lvlCSV
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	452 is_match <- isLevelSelected(fctr_lvl_1) && isLevelSelected(fctr_lvl_2)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	453 my_cor_cov <- do_detail_plot(
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	454 x_dataMatrix = my_matrix
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	455 , x_predictor = predictor
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	456 , x_is_match = is_match
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	457 , x_algorithm = algoC
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	458 , x_prefix = "Features"
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	459 , x_show_labels = labelFeatures
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	460 , x_show_loado_labels = labelOrthoFeatures
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	461 , x_progress = progress_action
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	462 , x_env = calc_env
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	463 )
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	464 if ( is.null(my_cor_cov) ) {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	465 progress_action("NOTHING TO PLOT")
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	466 } else {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	467 tsv <- my_cor_cov$tsv1
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	468 tsv$mz <- mz_lookup(tsv$featureID)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	469 tsv$rt <- rt_lookup(tsv$featureID)
1 e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	470 corcov_tsv_action(tsv)
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	471 did_plot <<- TRUE
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	472 }
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	473 }
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	474 #print("baz")
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	475 "dummy" # need to return a value; otherwise combn fails with an error
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	476 }
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	477 )
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	478 } else {
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	479 progress_action("NOTHING TO PLOT....")
e25fd8a13665 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94 eschen42 parents: 0 diff changeset	480 }
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	481 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	482 if (!did_plot) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	483 failure_action(sprintf("bad parameter! sampleMetadata must have at least two levels of factor '%s' matching '%s'", facC, originalLevCSV))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	484 return ( FALSE )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	485 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	486 return ( TRUE )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	487 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	488
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	489 # Calculate data for correlation-versus-covariance plot
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	490 # Adapted from:
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	491 # Wiklund_2008 doi:10.1021/ac0713510
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	492 # Galindo_Prieto_2014 doi:10.1002/cem.2627
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	493 # https://github.com/HegemanLab/extra_tools/blob/master/generic_PCA.R
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	494 cor_vs_cov <- function(matrix_x, ropls_x) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	495 x_class <- class(ropls_x)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	496 if ( !( as.character(x_class) == "opls" ) ) { # \|\| !( attr(class(x_class),"package") == "ropls" ) )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	497 stop( "cor_vs_cov: Expected ropls_x to be of class ropls::opls but instead it was of class ", as.character(x_class) )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	498 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	499 result <- list()
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	500 # suppLs$algoC - Character: algorithm used - "svd" for singular value decomposition; "nipals" for NIPALS
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	501 if ( ropls_x@suppLs$algoC == "nipals") {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	502 # Equations (1) and (2) from Supplement to Wiklund 2008, doi:10.1021/ac0713510
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	503 mag <- function(one_dimensional) sqrt(sum(one_dimensional * one_dimensional))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	504 mag_xi <- sapply(X = 1:ncol(matrix_x), FUN = function(x) mag(matrix_x[,x]))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	505 score_matrix <- ropls_x@scoreMN
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	506 score_matrix_transposed <- t(score_matrix)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	507 score_matrix_magnitude <- mag(score_matrix)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	508 result$covariance <- score_matrix_transposed %% matrix_x / ( score_matrix_magnitude score_matrix_magnitude )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	509 result$correlation <- score_matrix_transposed %% matrix_x / ( score_matrix_magnitude mag_xi )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	510 } else {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	511 # WARNING - untested code - I don't have test data to exercise this branch
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	512 # Equations (1) and (2) from Wiklund 2008, doi:10.1021/ac0713510
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	513 # scoreMN - Numerical matrix of x scores (T; dimensions: nrow(x) x predI) X = TP' + E; Y = TC' + F
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	514 score_matrix <- ropls_x@scoreMN
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	515 score_matrix_transposed <- t(score_matrix)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	516 cov_divisor <- nrow(matrix_x) - 1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	517 result$covariance <- sapply(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	518 X = 1:ncol(matrix_x)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	519 , FUN = function(x) score_matrix_transposed %*% matrix_x[,x] / cov_divisor
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	520 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	521 score_sd <- sapply(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	522 X = 1:ncol(score_matrix)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	523 , FUN = function(x) sd(score_matrix[,x])
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	524 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	525 # xSdVn - Numerical vector: variable standard deviations of the 'x' matrix
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	526 xSdVn <- ropls_x@xSdVn
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	527 result$correlation <- sapply(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	528 X = 1:ncol(matrix_x)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	529 , FUN = function(x) {
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	530 ( score_matrix_transposed / score_sd ) %% ( matrix_x[,x] / (xSdVn[x] cov_divisor) )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	531 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	532 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	533 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	534 result$correlation <- result$correlation[1,,drop = TRUE]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	535 result$covariance <- result$covariance[1,,drop = TRUE]
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	536
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	537 # Variant 4 of Variable Influence on Projection for OPLS from Galindo_Prieto_2014
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	538 # Length = number of features; labels = feature identifiers. (The same is true for $correlation and $covariance.)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	539 result$vip4p <- as.numeric(ropls_x@vipVn)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	540 result$vip4o <- as.numeric(ropls_x@orthoVipVn)
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	541 result$loadp <- as.numeric(ropls_x@loadingMN)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	542 result$loado <- as.numeric(ropls_x@orthoLoadingMN)
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	543 # get the level names
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	544 level_names <- sort(levels(as.factor(ropls_x@suppLs$y)))
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	545 fctr_lvl_1 <- level_names[1]
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	546 fctr_lvl_2 <- level_names[2]
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	547 feature_count <- length(ropls_x@vipVn)
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	548 result$level1 <- rep.int(x = fctr_lvl_1, times = feature_count)
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	549 result$level2 <- rep.int(x = fctr_lvl_2, times = feature_count)
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	550 # print(sprintf("sd(covariance) = %f; sd(correlation) = %f", sd(result$covariance), sd(result$correlation)))
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	551 superresult <- list()
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	552 if (length(result$vip4o) == 0) result$vip4o <- NA
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	553 greaterLevel <- sapply( X = result$correlation, FUN = function(my_corr) if ( my_corr < 0 ) fctr_lvl_1 else fctr_lvl_2 )
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	554 superresult$tsv1 <- data.frame(
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	555 featureID = names(ropls_x@vipVn)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	556 , factorLevel1 = result$level1
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	557 , factorLevel2 = result$level2
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	558 , greaterLevel = greaterLevel
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	559 , correlation = result$correlation
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	560 , covariance = result$covariance
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	561 , vip4p = result$vip4p
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	562 , vip4o = result$vip4o
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	563 , loadp = result$loadp
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	564 , loado = result$loado
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	565 , row.names = NULL
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	566 )
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	567 rownames(superresult$tsv1) <- superresult$tsv1$featureID
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	568 superresult$covariance <- result$covariance
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	569 superresult$correlation <- result$correlation
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	570 superresult$vip4p <- result$vip4p
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	571 superresult$vip4o <- result$vip4o
2 a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	572 superresult$loadp <- result$loadp
a06344808ffc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit ce5178ce51b80f242d24db555044e6afc530ac99 eschen42 parents: 1 diff changeset	573 superresult$loado <- result$loado
0 50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	574 superresult$details <- result
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	575 # #print(superresult$tsv1)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	576 result$superresult <- superresult
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	577 # Include thise in case future consumers of this routine want to use it in currently unanticipated ways
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	578 result$oplsda <- ropls_x
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	579 result$predictor <- ropls_x@suppLs$y # in case future consumers of this routine want to use it in currently unanticipated ways
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	580 return (superresult)
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	581 }
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	582
50a07adddfbd planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 52e588e19fe93d83d221710bb75559c5700ba637 eschen42 parents: diff changeset	583

Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov_calc.R @ 2:a06344808ffc draft