Mercurial > repos > iuc > ggplot2_pca

annotate ggplot2_pca.xml @ 5:23cadaaf734b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
author iuc
date Tue, 23 Nov 2021 07:54:23 +0000
parents 67cc04848f24
children 6d15608e230a
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23cadaaf734b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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1 <tool id="ggplot2_pca" name="PCA plot w ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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67cc04848f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <expand macro="bio_tools"/>
0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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23cadaaf734b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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7 <requirement type="package" version="0.4.13">r-ggfortify</requirement>
23cadaaf734b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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8 <requirement type="package" version="2.0.0">r-svglite</requirement>
0
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 cat '$script' &&
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12 Rscript '$script'
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="script"><![CDATA[
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16 @R_INIT@
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17
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18 ## Import libraries
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19 library(ggfortify)
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20 library(scales)
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21
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22 ## static VARs
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23 groups <- TRUE
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24 circles_boolean <- TRUE
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25 group_name <- list()
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26 group_cols <- list()
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27 group_colors <- list()
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28 group_feature <- ""
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29 group_colors_vector <- ""
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30
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31 input <- '$input1'
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32 header <- ${inputdata.header}
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33 rowname_index <- as.integer('$inputdata.row_names_index')
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34
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35 horizontal <- ${inputdata.sample_name_orientation}
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36 ## title <- '$title'
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37 transform <- '$adv.transform'
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38 ## background <- '$adv.theme'
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39 ## scaling <- '$adv.scaling.plot_scaling'
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40 ## legend <- '$adv.legend'
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41 group_type <- '$groups.group_type'
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42
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43 ##if(group_type == "define_groups"){
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44 #if str($groups.group_type) == "define_groups":
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45 #for $q in $groups.group_names:
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46 group_name <- append(group_name, '$q.groupName')
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47 group_cols <- append(group_cols, '$q.groupCols')
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48 group_colors <- append(group_colors, '$q.color_cond.plot_color')
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49 #end for
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50 #end if
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51 group_name <- unlist(group_name)
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52 group_cols <- unlist(group_cols)
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53 group_colors <- unlist(group_colors)
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54
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55 circles <- '$groups.circle'
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56 plot_param <- '$plotoptions'
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57
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58 ## split plotoptions
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59 plot_param_list <- strsplit(x = plot_param, split = ",")
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60 plot_options <- c("shape", "label") %in% plot_param_list[[1]]
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61
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62 ## read table with or with out header or row_names
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63 if(rowname_index > 0){
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64 df <- read.table(input, header = header, row.names = rowname_index, sep = "\t")
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65 }else{
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66 df <- read.table(input, header = header, sep = "\t")
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67 }
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68
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69 ## check if indices are out of range
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70 num_cols <- length(names(df))
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71 if(group_type == "define_groups"){
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72 check_col_indices <- as.integer(unlist(strsplit(group_cols, split = ",")))
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73 if(any(check_col_indices > num_cols)){
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74 stop("Error: column indices for grouping are out of range! Check help!")
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75 }
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76 }
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77
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78 ## check if table has only numbers
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79 if(any(!sapply(df, is.numeric))){
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80 stop("Error: table contains not only numbers!")
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81 }
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82
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83 ## check if group_names are unique
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84 if(length(unique(c(group_name, "no_group"))) != length(c(group_name, "no_group"))){
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85 stop("Error: group_names must be unique: ", paste(group_name, "no_group", collapse = ","), " is not unique!")
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86 }
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87
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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88 ## prepare group_features for grouping of samples accouring to orientation
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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89 if(horizontal){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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90 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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91 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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92 }else{
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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93 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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94 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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95 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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96
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 <- ""
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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98 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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99 ## 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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100 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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101 ## set up colors
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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102 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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103 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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104 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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105 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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106 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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107 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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108 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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109 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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110 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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111 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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112 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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113 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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114 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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115 names(gindex) <- gnames
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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116 gindex
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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117 })
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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118 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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119 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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120 ## 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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121 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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122 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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123 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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124 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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125
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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126 @LEGEND@
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127
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128 @XY_SCALING@
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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129
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130 @THEME@
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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131
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132 ## 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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133 if(horizontal){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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134 df <- as.data.frame(t(df))
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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137 plot_df <- df
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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138 ## 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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139 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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140 groups <- FALSE
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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141 }else{
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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142 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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143 group_name <- "group"
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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144 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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145
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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146 ## 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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147 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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148 circles_boolean <- FALSE
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149 }
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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150
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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151 plot_mat <- df
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152
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 ## transform dataset
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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154 if(transform == "log2"){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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155 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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156 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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157 }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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158 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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159 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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160 }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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161 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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162 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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163 }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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164 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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165 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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166 }else{
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167 plot_mat <- plot_mat
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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
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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170 ## 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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171 if(groups){
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172 if(circles_boolean){
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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173 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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174 frame = T, frame.type=circles, shape = plot_options[1],
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175 label = plot_options[2])
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176 }else{
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177 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, colour = group_name,
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178 frame = F, shape = plot_options[1], label = plot_options[2])
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179 }
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180 }else{
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181 if(!circles_boolean){
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182 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, frame = F, shape = plot_options[1], label = plot_options[2])
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183 }else{
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184 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, frame = F, shape = plot_options[1], label = plot_options[2])
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185 }
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186 }
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187
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188 ## add advanced plotting options for final plot
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189 plot_out <- plot_out +
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190 scale_color_manual(values=default_ggplot_colors) +
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191 scale_fill_manual(values=default_ggplot_colors) +
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192 gg_theme +
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193 gg_legend +
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194 ggtitle('$title') +
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195 theme(plot.title = element_text(hjust = 0.5))
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196
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197 @SAVE_OUTPUT@
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198 ]]></configfile>
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199 </configfiles>
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200 <inputs>
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201 <param name="input1" type="data" format="tabular" label="Select table"/>
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202 <conditional name="inputdata">
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203 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
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204 <option value="with_header" selected="true">Dataset with header</option>
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205 <option value="with_rownames">Dataset with row names</option>
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206 <option value="with_header_rownames">Dataset with header and row names</option>
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207 <option value="no_header_rownames">Dataset without header or row names</option>
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208 </param>
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209 <when value="with_header">
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210 <param name="header" type="hidden" value="TRUE"/>
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211 <param name="row_names_index" type="hidden" value="0"/>
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212 <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">
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213 <option value="TRUE" selected="true">horizontal</option>
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214 <option value="FALSE">vertial</option>
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215 </param>
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216 </when>
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217 <when value="with_rownames">
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218 <param name="header" type="hidden" value="FALSE"/>
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219 <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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220 <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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221 <option value="TRUE">horizontal</option>
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222 <option value="FALSE" selected="true">vertial</option>
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223 </param>
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224 </when>
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225 <when value="with_header_rownames">
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226 <param name="header" type="hidden" value="TRUE"/>
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227 <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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228 <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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229 <option value="TRUE" selected="true">horizontal</option>
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230 <option value="FALSE">vertial</option>
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231 </param>
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232 </when>
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233 <when value="no_header_rownames">
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234 <param name="header" type="hidden" value="FALSE"/>
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235 <param name="row_names_index" type="hidden" value="0"/>
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236 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
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237 </when>
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238 </conditional>
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239 <expand macro="title"/>
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240 <conditional name="groups">
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241 <param name="group_type" type="select" label="Select groups">
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242 <option value="no_groups" selected="true">No groups</option>
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243 <option value="define_groups">Define groups</option>
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244 </param>
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245 <when value="no_groups">
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246 <param name="circle" type="hidden" value="no"/>
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247 </when>
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diff changeset
248 <when value="define_groups">
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249 <repeat name="group_names" min="2" title="Group" help="Select the samples for this group">
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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250 <param name="groupName" type="text" optional="false" label="Group name"
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251 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)">
5
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252 <sanitizer invalid_char="">
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253 <valid initial="string.letters,string.digits">
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254 <add value=":" />
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255 <add value="-" />
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diff changeset
256 <add value=" " />
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diff changeset
257 <add value="_" />
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258 </valid>
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259 </sanitizer>
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diff changeset
260 <validator type="regex" message="Value may include alphanumeric characters, colons, dashes, underscores and spaces.">[0-9a-zA-Z:-_ ]+</validator>
0
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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261 </param>
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262 <param name="groupCols" type="data_column" data_ref="input1" multiple="true" min="1" label="Columns for group"
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263 help="WARNING: please use columns indices after removing the row name column if selected in second section!">
5
23cadaaf734b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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264 <validator type="regex" message="Select at least one column for each group!">[0-9a-zA-Z:-_ ]+</validator>
0
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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265 <!--<filter type="remove_value" meta_ref="groupCols" />-->
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266 </param>
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267 <conditional name="color_cond">
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268 <param name="color_bool" type="select" label="Change colors">
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269 <option value="default" selected="true">Default ggplot colors</option>
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270 <option value="selected_colors">Select colors</option>
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271 </param>
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272 <when value="selected_colors">
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273 <param name="plot_color" type="color" value="" label="Pick color">
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274 <sanitizer sanitize="false"/>
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275 </param>
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276 </when>
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277 <when value="default">
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278 <param name="plot_color" type="hidden" value="none"/>
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279 </when>
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280 </conditional>
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281 </repeat>
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282 <param name="circle" type="select" display="radio" multiple="false" label="Select type of ellipses">
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283 <option value="no">no ellipes</option>
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284 <option value="convex">convex</option>
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285 <option value="t" selected="true">t-distribution</option>
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286 <option value="norm">normal distribution</option>
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287 <option value="euclid">euclidean distance</option>
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288 </param>
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289 </when>
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290 </conditional>
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291 <param name="plotoptions" type="select" label="Select plot layout" display="radio" >
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292 <option value="shape" >show shapes</option>
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293 <option value="label" selected="true">show labels (group elements)</option>
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294 <option value="shape,label" >show shapes and labels</option>
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295 </param>
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296 <!-- Advanced Options -->
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297 <section name="adv" title="Advanced Options" expanded="false">
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298 <expand macro="transform"/>
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299 <expand macro="xy_scaling" />
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300 <expand macro="theme"/>
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301 <expand macro="legend"/>
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302 </section>
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303 <!-- Output Options -->
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304 <section name="out" title="Output Options" expanded="true">
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305 <expand macro="dimensions" />
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306 </section>
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307 </inputs>
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308 <outputs>
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309 <expand macro="additional_output" />
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310 </outputs>
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311 <tests>
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312 <test>
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313 <param name="input1" value="mtcars.txt" ftype="tabular"/>
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314 <conditional name="inputdata">
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315 <param name="input_type" value="with_header_rownames"/>
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316 <param name="header" value="TRUE"/>
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317 <param name="row_names_index" value="1"/>
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318 <param name="sample_name_orientation" value="TRUE"/>
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319 </conditional>
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320 <conditional name="groups">
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321 <param name="group_type" value="define_groups"/>
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322 <repeat name="group_names">
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323 <param name="groupName" value="group1"/>
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324 <param name="groupCols" value="3,4"/>
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325 <conditional name="color_cond">
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326 <param name="color_bool" value="default"/>
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327 <param name="plot_color" value="none"/>
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328 </conditional>
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329 </repeat>
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330 <repeat name="group_names">
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331 <param name="groupName" value="group2"/>
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332 <param name="groupCols" value="2,5,6,8,9,10,11"/>
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333 <conditional name="color_cond">
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334 <param name="color_bool" value="default"/>
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335 <param name="plot_color" value="none"/>
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336 </conditional>
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337 </repeat>
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338 <param name="circle" value="convex"/>
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339 </conditional>
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340 <param name="additional_output_format" value="pdf"/>
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341 <output name="output2" file="ggplot_pca_result1.pdf" compare="sim_size"/>
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342 </test>
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343 </tests>
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344 <help><![CDATA[
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345 **What it does**
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346
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347 This tool generates a Principal component analysis (PCA) for a given table using a combination of ggplot2 and ggfortify.
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348
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349 -----
e148543c622e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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350
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351 **Example**
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352
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353 **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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354
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355 **Example for row names in table**
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356
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357 +--------+-----------+-----------+---------------+---------------+
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358 | name | control 1 | control 2 | treatment 1 | treatment 2 |
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359 +========+===========+===========+===============+===============+
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360 | gene 1 | 10 | 12 | 3455 | 232 |
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361 +--------+-----------+-----------+---------------+---------------+
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362 | gene 2 | 20 | 2 | 345 | 334 |
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363 +--------+-----------+-----------+---------------+---------------+
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364 | gene 3 | 200 | 210 | 20 | 2 |
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365 +--------+-----------+-----------+---------------+---------------+
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366 | | | | | |
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367 +--------+-----------+-----------+---------------+---------------+
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368 | 1 | 2 | 3 | 4 | 5 |
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369 +--------+-----------+-----------+---------------+---------------+
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370
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371 The new index after reading the table will be:
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372
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373 +--------+-----------+-----------+--------------+---------------+
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374 | name | control 1 | control 2 | treatment 1 | treatment 2 |
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375 +========+===========+===========+==============+===============+
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376 |* | 1 | 2 | 3 | 4 |
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377 +--------+-----------+-----------+--------------+---------------+
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378
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379 -----
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380
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381 Pictures coming soon.
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382 ]]></help>
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383 <expand macro="citations">
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384 <citation type="bibtex">@article{tang2016ggfortify,
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385 title={ggfortify: unified interface to visualize statistical results of popular R packages},
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386 author={Tang, Yuan and Horikoshi, Masaaki and Li, Wenxuan},
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387 journal={The R Journal},
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388 volume={8},
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389 number={2},
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390 pages={478-489},
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391 year={2016},
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392 url = {https://journal.r-project.org/archive/2016/RJ-2016-060/RJ-2016-060.pdf}
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393 }
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394 </citation>
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395 <citation type="bibtex">@manual{gu2016getoptlong,
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396 title = {GetoptLong: Parsing Command-Line Arguments and Variable Interpolation},
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397 author = {Zuguang Gu},
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398 year = {2016},
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399 note = {R package version 0.1.5},
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400 url = {https://CRAN.R-project.org/package=GetoptLong},
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401 }
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402 </citation>
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403 </expand>
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404 </tool>