Mercurial > repos > iuc > ggplot2_point

annotate ggplot_point.xml @ 10:299307abd804 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
author iuc
date Thu, 24 Nov 2022 20:23:57 +0000
parents 1acf88921176
children d0fc8b746d57
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1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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e3a675da7fd0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit b9aa31ad4f99a9bbf726b78a0704ab1f68f05cea"
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2 <expand macro="bio_tools"/>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.0.0">r-svglite</requirement>
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8 </expand>
0
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9 <command detect_errors="exit_code"><![CDATA[
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10 cat '$script' &&
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11 Rscript '$script'
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="script"><![CDATA[
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15 @R_INIT@
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17 ## Import library
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18 library(ggplot2)
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20 @XY_SCALING@
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21
2
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22 @THEME@
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2
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24 @LEGEND@
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26 input <- read.csv('$input1', sep='\t', header=TRUE)
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28 ## renaming columns so ggplot can use them
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29 names(input)[$xplot] <- "xcol"
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30 names(input)[$yplot] <- "ycol"
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31
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32 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
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33 #if $adv.factor.factoring == "Multiple"
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34 gg_facet = facet_wrap( ~ factor)
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35 gg_factor = NULL
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36 color_scale = NULL
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37 #if $adv.type_conditional.points.pointoptions == "default"
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38 gg_point = geom_point(size=1, alpha=1, gg_factor)
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39 gg_line = geom_line(size=1, alpha=1, gg_factor)
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40 #else
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41 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
299307abd804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
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42 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
0
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43 #end if
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44
2
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45 names(input)[$adv.factor.factorcol] <- "factor"
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46
2
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47 #elif $adv.factor.factoring == "Single"
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48 gg_facet = NULL
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49 gg_factor = aes(colour=factor(factor))
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50
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51 #if $adv.type_conditional.points.pointoptions == "default"
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52 gg_point = geom_point(size=1, alpha=1, gg_factor)
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53 gg_line = geom_line(size=1, alpha=1, gg_factor)
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54 #else
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55 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor)
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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56 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor)
2
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57 #end if
0
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58
4
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59 #if $adv.factor.colororder == 1
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60 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
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61 #else
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62 color_scale = scale_color_brewer(palette='$adv.factor.colors', direction='$adv.factor.colororder')
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63 #end if
0
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64
2
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65 names(input)[$adv.factor.factorcol] <- "factor"
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66 #else
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67 gg_facet = NULL
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68 gg_factor = NULL
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69 color_scale = NULL
0
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70
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1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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71 #if $adv.type_conditional.points.pointoptions == "default"
2
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72 gg_point = geom_point(size=1, alpha=1, gg_factor)
4
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73 gg_line = geom_line(size=1, alpha=1, gg_factor)
2
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74 #else
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75 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
299307abd804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
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76 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
2
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77 #end if
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78 #end if
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80 @TRANSFORM@
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82 ##axis label custization
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83 #if $adv.axis_title_customization.axis_customization == "default"
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84 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
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85 #else
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86 gg_axistitle = theme(axis.title = element_text(color = '$adv.axis_text_customization.color', size = $adv.axis_text_customization.size, face = '$adv.axis_text_customization.face'))
0
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87 #end if
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88
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89 ##axis text(tick) custization
2
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90 #if $adv.axis_text_customization.axis_customization == "default"
0
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91 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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92 #else
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93 gg_axistext = theme(axis.text = element_text(color = '$adv.axis_text_customization.color', size = $adv.axis_text_customization.size, face = '$adv.axis_text_customization.face'))
0
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94 #end if
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95
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96 ##plot title custimization
2
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97 #if $adv.plot_title_customization.axis_customization == "default"
0
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98 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
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99 #else
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100 gg_plottitle = theme(plot.title = element_text(color='$adv.axis_text_customization.color', size=$adv.axis_text_customization.size, face='$adv.axis_text_customization.face'))
0
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101 #end if
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102
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103 ## grid line customization
2
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104 #if $adv.gridlinecust == "default"
0
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105 gg_gridline = NULL
2
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106 #elif $adv.gridlinecust == "hidemajor"
0
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107 gg_gridline = theme(panel.grid.major = element_blank())
2
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108 #elif $adv.gridlinecust == "hideminor"
0
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109 gg_gridline = theme(panel.grid.minor = element_blank())
2
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110 #elif $adv.gridlinecust == "hideboth"
0
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111 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
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112 #end if
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113
4
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114 ## choose between graph types (points/lines/both)
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115 #if $adv.type_conditional.type_options == "points"
4
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116 gg_line = NULL
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117 #elif $adv.type_conditional.type_options == "lines"
4
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118 gg_point = NULL
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119 #end if
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120
0
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121 #this is the actual ggplot command to make the final plot(s)
4
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122 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
2
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123 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
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124 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
0
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125
2
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126 @SAVE_OUTPUT@
0
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127 ]]></configfile>
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128 </configfiles>
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129 <inputs>
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130 <param name="input1" type="data" format="tabular" label="Input in tabular format" />
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131 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
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132 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
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133
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134 <expand macro="title" />
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135 <expand macro="xy_lab" />
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136 <section name="adv" title="Advanced options">
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137 <conditional name="type_conditional">
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138 <param name="type_options" type="select" label="Type of plot" >
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139 <option value="points">Points only (default)</option>
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140 <option value="lines">Lines only </option>
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141 <option value="pointslines">Points and Lines</option>
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142 </param>
9
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143 <when value ="points">
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144 <expand macro="points_options"/>
2
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145 </when>
9
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146 <when value="pointslines">
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147 <expand macro="points_options"/>
2
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148 </when>
9
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149 <when value="lines"/>
2
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150 </conditional>
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151 <conditional name="factor">
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152 <param name="factoring" type="select" label="Plotting multiple groups" >
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153 <option value="Default" selected="true">No thanks - just plot the data as one group</option>
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154 <option value="Single">Plot multiple groups of data on one plot</option>
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155 <option value="Multiple">Plot multiple groups of data on individual plots</option>
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156 </param>
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157 <when value="Default">
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158 <!--Do nothing here -->
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159 </when>
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160 <when value="Single">
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161 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" />
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162 <expand macro="colors" />
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163 <param name="colororder" type="select" label="Reverse color scheme" >
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164 <option value="1">Default order of color scheme</option>
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165 <option value="-1">Reverse the order of my color scheme</option>
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166 </param>
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167 </when>
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168 <when value="Multiple">
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169 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" />
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170 </when>
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171 </conditional>
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172 <conditional name="axis_title_customization">
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173 <expand macro="axis_customization" label="Axis title options" />
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174 </conditional>
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175 <conditional name="axis_text_customization">
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176 <expand macro="axis_customization" label="Axis text options" />
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177 </conditional>
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178 <conditional name="plot_title_customization">
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179 <expand macro="axis_customization" label="Plot title options" />
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180 </conditional>
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181 <param name="gridlinecust" type="select" label="Grid lines">
9
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182 <option value="default">Default grid lines</option>
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183 <option value="hidemajor">Hide major grid lines</option>
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184 <option value="hideminor">Hide minor grid lines</option>
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185 <option value="hideboth">Hide major and minor grid lines</option>
0
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186 </param>
2
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187 <expand macro="transform" />
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188 <expand macro="xy_scaling" />
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189 <expand macro="theme" />
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190 <expand macro="legend" />
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191 </section>
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192 <section name="out" title="Output Options" expanded="true">
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193 <expand macro="dimensions" />
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194 </section>
0
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195 </inputs>
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196 <outputs>
2
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197 <expand macro="additional_output" />
0
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198 </outputs>
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199 <tests>
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200 <test>
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201 <param name="input1" value="mtcars.txt" ftype="tabular" />
2
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202 <param name="additional_output_format" value="pdf" />
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203 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />
0
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204 </test>
9
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205 <!-- Test text options-->
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206 <test>
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207 <param name="input1" value="mtcars.txt" ftype="tabular" />
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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208 <section name="adv">
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209 <conditional name="type_conditional">
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210 <param name="type_options" value="points"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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211 <conditional name="points">
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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212 <param name="pointoptions" value="default"/>
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213 </conditional>
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214 </conditional>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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215 <conditional name="axis_text_customization">
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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216 <param name="axis_customization" value="defined"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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217 <param name="color" value="red"/>
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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218 </conditional>
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219 </section>
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220 <param name="additional_output_format" value="pdf" />
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221 <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" />
1acf88921176 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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222 </test>
10
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223 <!-- Test defined point options options-->
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224 <test>
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225 <param name="input1" value="mtcars.txt" ftype="tabular" />
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226 <section name="adv">
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227 <conditional name="type_conditional">
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228 <param name="type_options" value="points"/>
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229 <conditional name="points">
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230 <param name="pointoptions" value="defined"/>
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231 <param name="size" value="2"/>
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232 <param name="alpha" value="0.5"/>
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233 <param name="pointcolor" value="gold"/>
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234 <param name="shape" value="6"/>
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235 </conditional>
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236 </conditional>
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237 <conditional name="axis_text_customization">
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238 <param name="axis_customization" value="defined"/>
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239 <param name="color" value="red"/>
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240 </conditional>
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241 </section>
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242 <param name="additional_output_format" value="pdf" />
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243 <output name="output2" file="ggplot_point_result3.pdf" compare="sim_size" />
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244 </test>
0
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245 </tests>
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246 <help><![CDATA[
2
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247 This tool will generate a scatterplot representing data from two groups/conditions.
0
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248
2
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249 The input data should be in tabular format and the user can determine which groups (columns) to plot.
0
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250
9
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251 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "advanced - plotting multiple groups".
0
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252
2
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253 Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!
0
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254
9
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255 The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "advanced - output dimensions"
0
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256 ]]></help>
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257 <expand macro="citations"/>
1bff6682e780 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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258 </tool>