Mercurial > repos > proteore > proteore_heatmap_visualization

comparison heatmap_viz.R @ 3:07748b0136bb draft default tip

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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:18:07 -0400
parents 99207b432ebc
children
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2:99207b432ebc 3:07748b0136bb
1 #!/usr/bin/Rscript 1 #!/usr/bin/Rscript
2 options(warn=-1) #TURN OFF WARNINGS !!!!!!
2 3
3 suppressMessages(library('plotly',quietly = T)) 4 suppressMessages(library('plotly',quietly = T))
4 suppressMessages(library('heatmaply',quietly = T)) 5 suppressMessages(library('heatmaply',quietly = T))
5 6
6 #packageVersion('plotly') 7 #packageVersion('plotly')
78 #} 79 #}
79 return(uto) 80 return(uto)
80 } 81 }
81 82
82 get_cols <-function(input_cols) { 83 get_cols <-function(input_cols) {
83 input_cols <- gsub("c","",input_cols) 84 input_cols <- gsub("c","",gsub("C","",gsub(" ","",input_cols)))
84 if (grepl(":",input_cols)) { 85 if (grepl(":",input_cols)) {
85 first_col=unlist(strsplit(input_cols,":"))[1] 86 first_col=unlist(strsplit(input_cols,":"))[1]
86 last_col=unlist(strsplit(input_cols,":"))[2] 87 last_col=unlist(strsplit(input_cols,":"))[2]
87 cols=first_col:last_col 88 cols=first_col:last_col
88 } else { 89 } else {
100 header=str2bool(args$header) 101 header=str2bool(args$header)
101 output <- rapply(strsplit(args$output,"\\."),c) #remove extension 102 output <- rapply(strsplit(args$output,"\\."),c) #remove extension
102 output <- paste(output[1:length(output)-1],collapse=".") 103 output <- paste(output[1:length(output)-1],collapse=".")
103 output <- paste(output,args$type,sep=".") 104 output <- paste(output,args$type,sep=".")
104 cols = get_cols(args$cols) 105 cols = get_cols(args$cols)
105 rownames_col = as.integer(gsub("c","",args$row_names)) 106 rownames_col = as.integer(gsub("c","",gsub("C","",gsub(" ","",args$row_names))))
106 if (length(cols) <=1 ){ 107 if (length(cols) <=1 ){
107 stop("You need several colums to build a heatmap") 108 stop("You need several colums to build a heatmap")
108 } 109 }
109 dist=args$dist 110 dist=args$dist
110 clust=args$clust 111 clust=args$clust
114 uto <- read_file(args$input,header) 115 uto <- read_file(args$input,header)
115 uto <- clean_df(uto,cols,rownames_col) 116 uto <- clean_df(uto,cols,rownames_col)
116 uto <- uto[rowSums(is.na(uto)) != ncol(uto), ] #remove emptylines 117 uto <- uto[rowSums(is.na(uto)) != ncol(uto), ] #remove emptylines
117 118
118 if (header) { 119 if (header) {
119 col_names = names(data) 120 col_names = names(uto)
120 } else { 121 } else {
121 col_names = cols 122 col_names = cols
122 } 123 }
123 124
124 #building heatmap 125 #building heatmap