annotate ggplot2_pca.xml @ 9:ae344ccf9d62 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
author iuc
date Mon, 30 Sep 2024 15:40:34 +0000
parents b1268b7544d3
children
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fcb6a19960c6 "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">
0
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2 <macros>
c21099566418 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>
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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4 </macros>
9
ae344ccf9d62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
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5 <expand macro="bio_tools"/>
0
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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6 <requirements>
8
b1268b7544d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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7 <requirement type="package" version="0.4.14">r-ggfortify</requirement>
b1268b7544d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
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8 <requirement type="package" version="2.1.0">r-svglite</requirement>
0
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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9 </requirements>
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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10 <command detect_errors="exit_code"><![CDATA[
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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11 cat '$script' &&
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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12 Rscript '$script'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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13 ]]></command>
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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14 <configfiles>
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15 <configfile name="script"><![CDATA[
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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16 @R_INIT@
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17
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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18 ## Import libraries
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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19 library(ggfortify)
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20 library(scales)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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21
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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22 ## static VARs
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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23 groups <- TRUE
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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24 circles_boolean <- TRUE
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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25 group_name <- list()
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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26 group_cols <- list()
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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27 group_colors <- list()
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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28 group_feature <- ""
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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29 group_colors_vector <- ""
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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30
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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31 input <- '$input1'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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32 header <- ${inputdata.header}
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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33 rowname_index <- as.integer('$inputdata.row_names_index')
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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34
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35 horizontal <- ${inputdata.sample_name_orientation}
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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36 ## title <- '$title'
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37 transform <- '$adv.transform'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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38 ## background <- '$adv.theme'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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39 ## scaling <- '$adv.scaling.plot_scaling'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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40 ## legend <- '$adv.legend'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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41 group_type <- '$groups.group_type'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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42
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43 ##if(group_type == "define_groups"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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44 #if str($groups.group_type) == "define_groups":
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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, '$q.groupCols')
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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48 group_colors <- append(group_colors, '$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)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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'
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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57
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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")
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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65 }else{
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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66 df <- read.table(input, header = header, sep = "\t")
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67 }
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68
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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69 ## check if indices are out of range
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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70 num_cols <- length(names(df))
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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71 if(group_type == "define_groups"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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"))){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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
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88 ## prepare group_features for grouping of samples accouring to orientation
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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89 if(horizontal){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
90 num_cols <- length(names(df))
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
91 group_feature <- rep("no_group", num_cols)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
92 }else{
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
93 num_rows <- nrow(df)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
94 group_feature <- rep("no_group", num_rows)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
95 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
96
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
97 default_ggplot_colors <- ""
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
98 default_ggplot_colors_autoplot <- ""
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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diff changeset
99 ## split group elements and assign indexes
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
100 if(group_type == "define_groups"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
101 ## set up colors
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
102 color_names <- c(group_name, "no_group")
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
103 cat("\ncolor_names: ", color_names)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
104 default_ggplot_colors <- hue_pal()(length(color_names))
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
105 names(default_ggplot_colors) <- color_names
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
106 cat("\ndefault_ggplot_colors: ", default_ggplot_colors)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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107 names(group_colors) <- group_name
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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108 group_colors <- group_colors[group_colors != "none"]
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
109 default_ggplot_colors[names(group_colors)] <- group_colors
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
110 cat("\ndefault_ggplot_colors: ", default_ggplot_colors)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
111 group_string <- lapply(seq_along(group_name), function(k){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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112 gname <- group_name[k]
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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113 gindex <- as.integer(strsplit(group_cols[k], split = ",")[[1]])
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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114 gnames <- rep(gname, length(gindex))
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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115 names(gindex) <- gnames
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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116 gindex
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
117 })
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
118 group_string <- do.call(c, group_string)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
119 group_feature[group_string] <- names(group_string)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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120 ## subset colors on groups if and check if there is "no_group" present
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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121 default_ggplot_colors <- default_ggplot_colors[unique(group_feature)]
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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122 default_ggplot_colors_autoplot <- default_ggplot_colors[group_feature]
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
123 cat("\ndefault_ggplot_colors: ", default_ggplot_colors)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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124 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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125
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
126 @LEGEND@
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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127
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
128 @XY_SCALING@
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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129
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
130 @THEME@
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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131
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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132 ## transpose data.frame for plotting if sample names are horizontal
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
133 if(horizontal){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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134 df <- as.data.frame(t(df))
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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135 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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136
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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diff changeset
137 plot_df <- df
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
138 ## set group column if wanted
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
139 if(group_type %in% "no_groups"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
140 groups <- FALSE
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
141 }else{
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
142 plot_df\$group <- group_feature
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
143 group_name <- "group"
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
144 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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145
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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146 ## set boolean elipes_value to plot circle options
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
147 if(circles %in% "no"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
diff changeset
148 circles_boolean <- FALSE
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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149 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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150
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
151 plot_mat <- df
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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152
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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153 ## transform dataset
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
154 if(transform == "log2"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
155 plot_mat <- log2(plot_mat)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
156 cat("\n ", transform, " transformed")
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
157 }else if(transform == "log2plus1"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
158 plot_mat <- log2(plot_mat+1)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
159 cat("\n ", transform, " transformed")
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
160 }else if(transform == "log10"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
161 plot_mat <- log10(plot_mat)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
162 cat("\n ", transform, " transformed")
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
163 }else if(transform == "log10plus1"){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
164 plot_mat <- log10(plot_mat+1)
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
165 cat("\n ", transform, " transformed")
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
166 }else{
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
167 plot_mat <- plot_mat
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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168 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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169
c21099566418 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
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
171 if(groups){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
172 if(circles_boolean){
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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173 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, colour = group_name,
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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174 frame = T, frame.type=circles, shape = plot_options[1],
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
175 label = plot_options[2])
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
diff changeset
176 }else{
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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parents:
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177 plot_out <- autoplot(prcomp(plot_mat), data = plot_df, colour = group_name,
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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178 frame = F, shape = plot_options[1], label = plot_options[2])
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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179 }
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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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"/>
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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">
c21099566418 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"/>
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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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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">
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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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256 <add value=" " />
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257 <add value="_" />
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258 </valid>
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259 </sanitizer>
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260 <validator type="regex" message="Value may include alphanumeric characters, colons, dashes, underscores and spaces.">[0-9a-zA-Z:-_ ]+</validator>
0
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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"
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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263 help="WARNING: please use columns indices after removing the row name column if selected in second section!">
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264 <validator type="regex" message="Select at least one column for each group!">[0-9a-zA-Z:-_ ]+</validator>
0
c21099566418 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">
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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 expect_num_outputs="2">
0
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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" ftype="pdf" compare="sim_size"/>
0
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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 -----
c21099566418 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**
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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 +--------+-----------+-----------+---------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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358 | name | control 1 | control 2 | treatment 1 | treatment 2 |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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359 +========+===========+===========+===============+===============+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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360 | gene 1 | 10 | 12 | 3455 | 232 |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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361 +--------+-----------+-----------+---------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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362 | gene 2 | 20 | 2 | 345 | 334 |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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363 +--------+-----------+-----------+---------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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364 | gene 3 | 200 | 210 | 20 | 2 |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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365 +--------+-----------+-----------+---------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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366 | | | | | |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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367 +--------+-----------+-----------+---------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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368 | 1 | 2 | 3 | 4 | 5 |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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369 +--------+-----------+-----------+---------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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370
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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371 The new index after reading the table will be:
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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372
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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373 +--------+-----------+-----------+--------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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374 | name | control 1 | control 2 | treatment 1 | treatment 2 |
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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375 +========+===========+===========+==============+===============+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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376 |* | 1 | 2 | 3 | 4 |
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377 +--------+-----------+-----------+--------------+---------------+
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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378
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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379 -----
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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380
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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381 Pictures coming soon.
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382 ]]></help>
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383 <expand macro="citations">
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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384 <citation type="bibtex">@article{tang2016ggfortify,
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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},
c21099566418 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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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>