Mercurial > repos > iuc > ggplot2_pca

annotate ggplot2_pca.xml @ 3:f3e4904e039a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 8e0f13edc2c06772dac0c1258e362045e68028b8"
author iuc
date Wed, 18 Nov 2020 21:31:07 +0000
parents e148543c622e
children 67cc04848f24
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e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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1 <tool id="ggplot2_pca" name="PCA plot w ggplot2" version="@VERSION@">
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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2 <macros>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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3 <import>macros.xml</import>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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4 </macros>
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5 <requirements>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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6 <requirement type="package" version="0.4.3">r-ggfortify</requirement>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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7 <requirement type="package" version="1.2.1">r-svglite</requirement>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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8 </requirements>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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9 <command detect_errors="exit_code"><![CDATA[
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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10 cat '$script' &&
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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11 Rscript '$script'
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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12 ]]></command>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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13 <configfiles>
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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14 <configfile name="script"><![CDATA[
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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15 @R_INIT@
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16
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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17 ## Import libraries
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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18 library(ggfortify)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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19 library(scales)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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20
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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21 ## static VARs
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22 groups <- TRUE
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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23 circles_boolean <- TRUE
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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24 group_name <- list()
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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25 group_cols <- list()
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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26 group_colors <- list()
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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27 group_feature <- ""
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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28 group_colors_vector <- ""
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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29
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30 input <- '$input1'
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 header <- ${inputdata.header}
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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32 rowname_index <- as.integer('$inputdata.row_names_index')
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33
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34 horizontal <- ${inputdata.sample_name_orientation}
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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35 ## title <- '$title'
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36 transform <- '$adv.transform'
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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37 ## background <- '$adv.theme'
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38 ## scaling <- '$adv.scaling.plot_scaling'
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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39 ## legend <- '$adv.legend'
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 group_type <- '$groups.group_type'
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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41
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42 ##if(group_type == "define_groups"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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43 #if str($groups.group_type) == "define_groups":
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44 #for $q in $groups.group_names:
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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45 group_name <- append(group_name, '$q.groupName')
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46 group_cols <- append(group_cols, '$q.groupCols')
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47 group_colors <- append(group_colors, '$q.color_cond.plot_color')
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48 #end for
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49 #end if
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50 group_name <- unlist(group_name)
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51 group_cols <- unlist(group_cols)
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52 group_colors <- unlist(group_colors)
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53
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54 circles <- '$groups.circle'
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55 plot_param <- '$plotoptions'
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56
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57 ## split plotoptions
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58 plot_param_list <- strsplit(x = plot_param, split = ",")
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59 plot_options <- c("shape", "label") %in% plot_param_list[[1]]
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60
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61 ## read table with or with out header or row_names
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62 if(rowname_index > 0){
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63 df <- read.table(input, header = header, row.names = rowname_index, sep = "\t")
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64 }else{
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65 df <- read.table(input, header = header, sep = "\t")
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66 }
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67
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68 ## check if indices are out of range
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69 num_cols <- length(names(df))
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70 if(group_type == "define_groups"){
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71 check_col_indices <- as.integer(unlist(strsplit(group_cols, split = ",")))
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72 if(any(check_col_indices > num_cols)){
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73 stop("Error: column indices for grouping are out of range! Check help!")
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74 }
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75 }
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76
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77 ## check if table has only numbers
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78 if(any(!sapply(df, is.numeric))){
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79 stop("Error: table contains not only numbers!")
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80 }
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81
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82 ## check if group_names are unique
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83 if(length(unique(c(group_name, "no_group"))) != length(c(group_name, "no_group"))){
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84 stop("Error: group_names must be unique: ", paste(group_name, "no_group", collapse = ","), " is not unique!")
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85 }
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86
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87 ## prepare group_features for grouping of samples accouring to orientation
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88 if(horizontal){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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89 num_cols <- length(names(df))
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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90 group_feature <- rep("no_group", num_cols)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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91 }else{
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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92 num_rows <- nrow(df)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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93 group_feature <- rep("no_group", num_rows)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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94 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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95
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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96 default_ggplot_colors <- ""
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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97 default_ggplot_colors_autoplot <- ""
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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98 ## split group elements and assign indexes
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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99 if(group_type == "define_groups"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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100 ## set up colors
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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101 color_names <- c(group_name, "no_group")
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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102 cat("\ncolor_names: ", color_names)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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103 default_ggplot_colors <- hue_pal()(length(color_names))
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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104 names(default_ggplot_colors) <- color_names
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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105 cat("\ndefault_ggplot_colors: ", default_ggplot_colors)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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106 names(group_colors) <- group_name
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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107 group_colors <- group_colors[group_colors != "none"]
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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108 default_ggplot_colors[names(group_colors)] <- group_colors
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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109 cat("\ndefault_ggplot_colors: ", default_ggplot_colors)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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110 group_string <- lapply(seq_along(group_name), function(k){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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111 gname <- group_name[k]
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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112 gindex <- as.integer(strsplit(group_cols[k], split = ",")[[1]])
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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113 gnames <- rep(gname, length(gindex))
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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114 names(gindex) <- gnames
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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115 gindex
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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116 })
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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117 group_string <- do.call(c, group_string)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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118 group_feature[group_string] <- names(group_string)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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119 ## subset colors on groups if and check if there is "no_group" present
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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120 default_ggplot_colors <- default_ggplot_colors[unique(group_feature)]
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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121 default_ggplot_colors_autoplot <- default_ggplot_colors[group_feature]
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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122 cat("\ndefault_ggplot_colors: ", default_ggplot_colors)
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123 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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124
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125 @LEGEND@
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126
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127 @XY_SCALING@
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128
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129 @THEME@
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130
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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131 ## transpose data.frame for plotting if sample names are horizontal
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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132 if(horizontal){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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133 df <- as.data.frame(t(df))
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134 }
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135
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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136 plot_df <- df
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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137 ## set group column if wanted
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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138 if(group_type %in% "no_groups"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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139 groups <- FALSE
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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140 }else{
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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141 plot_df\$group <- group_feature
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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142 group_name <- "group"
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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143 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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144
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145 ## set boolean elipes_value to plot circle options
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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146 if(circles %in% "no"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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147 circles_boolean <- FALSE
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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148 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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149
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150 plot_mat <- df
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151
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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152 ## transform dataset
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 if(transform == "log2"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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154 plot_mat <- log2(plot_mat)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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155 cat("\n ", transform, " transformed")
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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156 }else if(transform == "log2plus1"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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157 plot_mat <- log2(plot_mat+1)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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158 cat("\n ", transform, " transformed")
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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159 }else if(transform == "log10"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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160 plot_mat <- log10(plot_mat)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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161 cat("\n ", transform, " transformed")
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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162 }else if(transform == "log10plus1"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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163 plot_mat <- log10(plot_mat+1)
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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164 cat("\n ", transform, " transformed")
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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165 }else{
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166 plot_mat <- plot_mat
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167 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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168
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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169 ## plot with or without groups and set more plotting options using autoplot
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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170 if(groups){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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171 if(circles_boolean){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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172 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, colour = group_name,
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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173 frame = T, frame.type=circles, shape = plot_options[1],
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174 label = plot_options[2])
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175 }else{
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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176 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, colour = group_name,
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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177 frame = F, shape = plot_options[1], label = plot_options[2])
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178 }
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179 }else{
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180 if(!circles_boolean){
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181 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, frame = F, shape = plot_options[1], label = plot_options[2])
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182 }else{
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183 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, frame = F, shape = plot_options[1], label = plot_options[2])
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184 }
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185 }
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186
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187 ## add advanced plotting options for final plot
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188 plot_out <- plot_out +
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189 scale_color_manual(values=default_ggplot_colors) +
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190 scale_fill_manual(values=default_ggplot_colors) +
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191 gg_theme +
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192 gg_legend +
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193 ggtitle('$title') +
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194 theme(plot.title = element_text(hjust = 0.5))
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195
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196 @SAVE_OUTPUT@
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197 ]]></configfile>
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198 </configfiles>
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199 <inputs>
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200 <param name="input1" type="data" format="tabular" label="Select table"/>
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201 <conditional name="inputdata">
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202 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
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203 <option value="with_header" selected="true">Dataset with header</option>
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204 <option value="with_rownames">Dataset with row names</option>
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205 <option value="with_header_rownames">Dataset with header and row names</option>
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206 <option value="no_header_rownames">Dataset without header or row names</option>
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207 </param>
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208 <when value="with_header">
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209 <param name="header" type="hidden" value="TRUE"/>
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210 <param name="row_names_index" type="hidden" value="0"/>
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211 <param name="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names">
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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212 <option value="TRUE" selected="true">horizontal</option>
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213 <option value="FALSE">vertial</option>
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214 </param>
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215 </when>
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216 <when value="with_rownames">
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217 <param name="header" type="hidden" value="FALSE"/>
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218 <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
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219 <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
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220 <option value="TRUE">horizontal</option>
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221 <option value="FALSE" selected="true">vertial</option>
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222 </param>
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223 </when>
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224 <when value="with_header_rownames">
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225 <param name="header" type="hidden" value="TRUE"/>
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226 <param name="row_names_index" label="Select column, for row names" type="data_column" data_ref="input1" help="WARNING: please consider that using row names might shift the grouping columns"/>
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227 <param name="sample_name_orientation" type="select" label="Sample names orientation" display="radio" multiple="false" help="deside whether header names or row names are interpreted as sample names">
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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228 <option value="TRUE" selected="true">horizontal</option>
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229 <option value="FALSE">vertial</option>
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230 </param>
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231 </when>
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232 <when value="no_header_rownames">
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233 <param name="header" type="hidden" value="FALSE"/>
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234 <param name="row_names_index" type="hidden" value="0"/>
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235 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
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236 </when>
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237 </conditional>
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238 <expand macro="title"/>
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239 <conditional name="groups">
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240 <param name="group_type" type="select" label="Select groups">
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241 <option value="no_groups" selected="true">No groups</option>
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242 <option value="define_groups">Define groups</option>
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243 </param>
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244 <when value="no_groups">
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245 <param name="circle" type="hidden" value="no"/>
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246 </when>
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247 <when value="define_groups">
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248 <repeat name="group_names" min="2" title="Group" help="Select the samples for this group">
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249 <param name="groupName" type="text" optional="false" label="Group name"
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250 help="Use short names, avoid special characters and numbers at the beginning of the name (The names might be changed by the program to make them conform to processing in R)">
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251 <validator type="no_options" message="Please choose a name for this group!"/>
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252 </param>
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253 <param name="groupCols" type="data_column" data_ref="input1" multiple="true" min="1" label="Columns for group"
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254 help="WARNING: please use columns indices after removing the row name column if selected in second section!">
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255 <validator type="no_options" message="Select at least one column for each group!"/>
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256 <!--<filter type="remove_value" meta_ref="groupCols" />-->
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257 </param>
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258 <conditional name="color_cond">
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259 <param name="color_bool" type="select" label="Change colors">
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260 <option value="default" selected="true">Default ggplot colors</option>
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261 <option value="selected_colors">Select colors</option>
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262 </param>
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263 <when value="selected_colors">
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264 <param name="plot_color" type="color" value="" label="Pick color">
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265 <sanitizer sanitize="false"/>
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266 </param>
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267 </when>
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268 <when value="default">
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269 <param name="plot_color" type="hidden" value="none"/>
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270 </when>
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271 </conditional>
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272 </repeat>
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273 <param name="circle" type="select" display="radio" multiple="false" label="Select type of ellipses">
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274 <option value="no">no ellipes</option>
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275 <option value="convex">convex</option>
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276 <option value="t" selected="true">t-distribution</option>
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277 <option value="norm">normal distribution</option>
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278 <option value="euclid">euclidean distance</option>
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279 </param>
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280 </when>
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281 </conditional>
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282 <param name="plotoptions" type="select" label="Select plot layout" display="radio" >
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283 <option value="shape" >show shapes</option>
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284 <option value="label" selected="true">show labels (group elements)</option>
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285 <option value="shape,label" >show shapes and labels</option>
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286 </param>
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287 <!-- Advanced Options -->
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288 <section name="adv" title="Advanced Options" expanded="false">
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289 <expand macro="transform"/>
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290 <expand macro="xy_scaling" />
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291 <expand macro="theme"/>
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292 <expand macro="legend"/>
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293 </section>
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294 <!-- Output Options -->
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295 <section name="out" title="Output Options" expanded="true">
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296 <expand macro="dimensions" />
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297 </section>
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298 </inputs>
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299 <outputs>
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300 <expand macro="additional_output" />
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301 </outputs>
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302 <tests>
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303 <test>
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304 <param name="input1" value="mtcars.txt" ftype="tabular"/>
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305 <conditional name="inputdata">
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306 <param name="input_type" value="with_header_rownames"/>
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307 <param name="header" value="TRUE"/>
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308 <param name="row_names_index" value="1"/>
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309 <param name="sample_name_orientation" value="TRUE"/>
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310 </conditional>
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311 <conditional name="groups">
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312 <param name="group_type" value="define_groups"/>
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313 <repeat name="group_names">
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314 <param name="groupName" value="group1"/>
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315 <param name="groupCols" value="3,4"/>
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316 <conditional name="color_cond">
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317 <param name="color_bool" value="default"/>
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318 <param name="plot_color" value="none"/>
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319 </conditional>
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320 </repeat>
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321 <repeat name="group_names">
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322 <param name="groupName" value="group2"/>
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323 <param name="groupCols" value="2,5,6,8,9,10,11"/>
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324 <conditional name="color_cond">
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325 <param name="color_bool" value="default"/>
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326 <param name="plot_color" value="none"/>
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327 </conditional>
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328 </repeat>
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329 <param name="circle" value="convex"/>
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330 </conditional>
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331 <param name="additional_output_format" value="pdf"/>
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332 <output name="output2" file="ggplot_pca_result1.pdf" compare="sim_size"/>
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333 </test>
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334 </tests>
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335 <help><![CDATA[
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336 **What it does**
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337
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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338 This tool generates a Principal component analysis (PCA) for a given table using a combination of ggplot2 and ggfortify.
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339
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340 -----
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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341
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342 **Example**
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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343
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344 **WARNING:** Be carefull when selecting row names in the second option because the grouping elements do not update automaticly before executing the script. This means that columns have to be chosen as if the row name column was already be removed.
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345
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346 **Example for row names in table**
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347
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348 +--------+-----------+-----------+---------------+---------------+
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349 | name | control 1 | control 2 | treatment 1 | treatment 2 |
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350 +========+===========+===========+===============+===============+
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351 | gene 1 | 10 | 12 | 3455 | 232 |
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352 +--------+-----------+-----------+---------------+---------------+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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353 | gene 2 | 20 | 2 | 345 | 334 |
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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354 +--------+-----------+-----------+---------------+---------------+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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355 | gene 3 | 200 | 210 | 20 | 2 |
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356 +--------+-----------+-----------+---------------+---------------+
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357 | | | | | |
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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358 +--------+-----------+-----------+---------------+---------------+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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359 | 1 | 2 | 3 | 4 | 5 |
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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360 +--------+-----------+-----------+---------------+---------------+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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361
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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362 The new index after reading the table will be:
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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363
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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364 +--------+-----------+-----------+--------------+---------------+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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365 | name | control 1 | control 2 | treatment 1 | treatment 2 |
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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366 +========+===========+===========+==============+===============+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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367 |* | 1 | 2 | 3 | 4 |
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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368 +--------+-----------+-----------+--------------+---------------+
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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369
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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370 -----
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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371
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372 Pictures coming soon.
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373 ]]></help>
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374 <expand macro="citations">
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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375 <citation type="bibtex">@article{tang2016ggfortify,
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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376 title={ggfortify: unified interface to visualize statistical results of popular R packages},
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377 author={Tang, Yuan and Horikoshi, Masaaki and Li, Wenxuan},
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378 journal={The R Journal},
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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379 volume={8},
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380 number={2},
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381 pages={478-489},
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382 year={2016},
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383 url = {https://journal.r-project.org/archive/2016/RJ-2016-060/RJ-2016-060.pdf}
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384 }
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385 </citation>
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386 <citation type="bibtex">@manual{gu2016getoptlong,
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387 title = {GetoptLong: Parsing Command-Line Arguments and Variable Interpolation},
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388 author = {Zuguang Gu},
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389 year = {2016},
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390 note = {R package version 0.1.5},
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391 url = {https://CRAN.R-project.org/package=GetoptLong},
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392 }
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393 </citation>
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394 </expand>
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395 </tool>