Mercurial > repos > iuc > ggplot2_point

comparison ggplot_point.xml @ 9:1acf88921176 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
author iuc
date Tue, 23 Nov 2021 07:58:14 +0000
parents e3a675da7fd0
children 299307abd804
comparison
equal deleted inserted replaced
8:e3a675da7fd0 9:1acf88921176
1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@VERSION@+galaxy2" profile="18.01"> 1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <expand macro="bio_tools"/> 2 <expand macro="bio_tools"/>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.2.1">r-svglite</requirement> 7 <requirement type="package" version="2.0.0">r-svglite</requirement>
8 </expand> 8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 cat '$script' && 10 cat '$script' &&
11 Rscript '$script' 11 Rscript '$script'
12 ]]></command> 12 ]]></command>
32 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots 32 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
33 #if $adv.factor.factoring == "Multiple" 33 #if $adv.factor.factoring == "Multiple"
34 gg_facet = facet_wrap( ~ factor) 34 gg_facet = facet_wrap( ~ factor)
35 gg_factor = NULL 35 gg_factor = NULL
36 color_scale = NULL 36 color_scale = NULL
37 #if $adv.points.pointoptions == "default" 37 #if $adv.type_conditional.points.pointoptions == "default"
38 gg_point = geom_point(size=1, alpha=1, gg_factor) 38 gg_point = geom_point(size=1, alpha=1, gg_factor)
39 gg_line = geom_line(size=1, alpha=1, gg_factor) 39 gg_line = geom_line(size=1, alpha=1, gg_factor)
40 #else 40 #else
41 gg_point = geom_point(size=$adv.points.size, alpha=$adv.points.alpha, colour='$adv.points.pointcolor') 41 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor')
42 gg_line = geom_line(size=$adv.points.size, alpha=$adv.points.alpha, colour='$adv.points.pointcolor') 42 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor')
43 #end if 43 #end if
44 44
45 names(input)[$adv.factor.factorcol] <- "factor" 45 names(input)[$adv.factor.factorcol] <- "factor"
46 46
47 #elif $adv.factor.factoring == "Single" 47 #elif $adv.factor.factoring == "Single"
48 gg_facet = NULL 48 gg_facet = NULL
49 gg_factor = aes(colour=factor(factor)) 49 gg_factor = aes(colour=factor(factor))
50 50
51 #if $adv.points.pointoptions == "default" 51 #if $adv.type_conditional.points.pointoptions == "default"
52 gg_point = geom_point(size=1, alpha=1, gg_factor) 52 gg_point = geom_point(size=1, alpha=1, gg_factor)
53 gg_line = geom_line(size=1, alpha=1, gg_factor) 53 gg_line = geom_line(size=1, alpha=1, gg_factor)
54 #else 54 #else
55 gg_point = geom_point(size=$adv.points.size, alpha=$adv.points.alpha, gg_factor) 55 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor)
56 gg_line = geom_line(size=$adv.points.size, alpha=$adv.points.alpha, gg_factor) 56 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor)
57 #end if 57 #end if
58 58
59 #if $adv.factor.colororder == 1 59 #if $adv.factor.colororder == 1
60 color_scale = scale_colour_hue(direction='$adv.factor.colororder') 60 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
61 #else 61 #else
66 #else 66 #else
67 gg_facet = NULL 67 gg_facet = NULL
68 gg_factor = NULL 68 gg_factor = NULL
69 color_scale = NULL 69 color_scale = NULL
70 70
71 #if $adv.points.pointoptions == "default" 71 #if $adv.type_conditional.points.pointoptions == "default"
72 gg_point = geom_point(size=1, alpha=1, gg_factor) 72 gg_point = geom_point(size=1, alpha=1, gg_factor)
73 gg_line = geom_line(size=1, alpha=1, gg_factor) 73 gg_line = geom_line(size=1, alpha=1, gg_factor)
74 #else 74 #else
75 gg_point = geom_point(size=$adv.points.size, alpha=$adv.points.alpha, colour='$adv.points.pointcolor') 75 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor')
76 gg_line = geom_line(size=$adv.points.size, alpha=$adv.points.alpha, colour='$adv.points.pointcolor') 76 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor')
77 #end if 77 #end if
78 #end if 78 #end if
79 79
80 @TRANSFORM@ 80 @TRANSFORM@
81 81
82 ##axis label custization 82 ##axis label custization
83 #if $adv.axis_title_customization.axis_customization == "default" 83 #if $adv.axis_title_customization.axis_customization == "default"
84 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL)) 84 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
85 #else 85 #else
86 gg_axistitle = theme(axis.title = element_text(color = '$adv.color', size = $adv.size, face = '$adv.face')) 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'))
87 #end if 87 #end if
88 88
89 ##axis text(tick) custization 89 ##axis text(tick) custization
90 #if $adv.axis_text_customization.axis_customization == "default" 90 #if $adv.axis_text_customization.axis_customization == "default"
91 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL)) 91 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
92 #else 92 #else
93 gg_axistext = theme(axis.text = element_text(color = '$adv.color', size = $adv.size, face = '$adv.face')) 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'))
94 #end if 94 #end if
95 95
96 ##plot title custimization 96 ##plot title custimization
97 #if $adv.plot_title_customization.axis_customization == "default" 97 #if $adv.plot_title_customization.axis_customization == "default"
98 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL)) 98 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
99 #else 99 #else
100 gg_plottitle = theme(plot.title = element_text(color='$adv.color', size=$adv.size, face='$adv.face')) 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'))
101 #end if 101 #end if
102 102
103 ## grid line customization 103 ## grid line customization
104 #if $adv.gridlinecust == "default" 104 #if $adv.gridlinecust == "default"
105 gg_gridline = NULL 105 gg_gridline = NULL
110 #elif $adv.gridlinecust == "hideboth" 110 #elif $adv.gridlinecust == "hideboth"
111 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank()) 111 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
112 #end if 112 #end if
113 113
114 ## choose between graph types (points/lines/both) 114 ## choose between graph types (points/lines/both)
115 #if $adv.type == "points" 115 #if $adv.type_conditional.type_options == "points"
116 gg_line = NULL 116 gg_line = NULL
117 #elif $adv.type == "lines" 117 #elif $adv.type_conditional.type_options == "lines"
118 gg_point = NULL 118 gg_point = NULL
119 #end if 119 #end if
120 120
121 #this is the actual ggplot command to make the final plot(s) 121 #this is the actual ggplot command to make the final plot(s)
122 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet + 122 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
131 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" /> 131 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
132 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" /> 132 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
133 133
134 <expand macro="title" /> 134 <expand macro="title" />
135 <expand macro="xy_lab" /> 135 <expand macro="xy_lab" />
136 <section name="adv" title="Advanced Options" expanded="false"> 136 <section name="adv" title="Advanced options">
137 <param name="type" type="select" label="Type of plot" > 137 <conditional name="type_conditional">
138 <option value="points">Points only (default)</option> 138 <param name="type_options" type="select" label="Type of plot" >
139 <option value="lines">Lines only </option> 139 <option value="points">Points only (default)</option>
140 <option value="pointslines">Points and Lines</option> 140 <option value="lines">Lines only </option>
141 </param> 141 <option value="pointslines">Points and Lines</option>
142 <conditional name="points">
143 <param name="pointoptions" type="select" label="Data point options">
144 <option value="default" selected="true">Default</option>
145 <option value="defined">User defined point options</option>
146 </param> 142 </param>
147 <when value="default"> 143 <when value ="points">
148 <!--Do nothing here --> 144 <expand macro="points_options"/>
149 </when> 145 </when>
150 <when value="defined"> 146 <when value="pointslines">
151 <param name="size" type="float" value="1" label="relative size of points" /> 147 <expand macro="points_options"/>
152 <param name="alpha" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" /> 148 </when>
153 <param name="pointcolor" type="select" label="Color of data points" > 149 <when value="lines"/>
154 <option value="black">Black (default)</option>
155 <option value="red">Red</option>
156 <option value="white">White</option>
157 <option value="blue">Blue</option>
158 <option value="orange">Orange</option>
159 <option value="yellow">Yellow</option>
160 <option value="green">Green</option>
161 <option value="purple">Purple</option>
162 <option value="magenta">Magenta</option>
163 <option value="cyan">Cyan</option>
164 <option value="grey">Grey</option>
165 <option value="gold">Gold</option>
166 </param>
167 </when>
168 </conditional> 150 </conditional>
169 <conditional name="factor"> 151 <conditional name="factor">
170 <param name="factoring" type="select" label="Plotting multiple groups" > 152 <param name="factoring" type="select" label="Plotting multiple groups" >
171 <option value="Default" selected="true">No thanks - just plot the data as one group</option> 153 <option value="Default" selected="true">No thanks - just plot the data as one group</option>
172 <option value="Single">Plot multiple groups of data on one plot</option> 154 <option value="Single">Plot multiple groups of data on one plot</option>
195 </conditional> 177 </conditional>
196 <conditional name="plot_title_customization"> 178 <conditional name="plot_title_customization">
197 <expand macro="axis_customization" label="Plot title options" /> 179 <expand macro="axis_customization" label="Plot title options" />
198 </conditional> 180 </conditional>
199 <param name="gridlinecust" type="select" label="Grid lines"> 181 <param name="gridlinecust" type="select" label="Grid lines">
200 <option value="default">Default grid lines</option> 182 <option value="default">Default grid lines</option>
201 <option value="hidemajor">Hide major grid lines</option> 183 <option value="hidemajor">Hide major grid lines</option>
202 <option value="hideminor">Hide minor grid lines</option> 184 <option value="hideminor">Hide minor grid lines</option>
203 <option value="hideboth">Hide major and minor grid lines</option> 185 <option value="hideboth">Hide major and minor grid lines</option>
204 </param> 186 </param>
205 <expand macro="transform" /> 187 <expand macro="transform" />
206 <expand macro="xy_scaling" /> 188 <expand macro="xy_scaling" />
207 <expand macro="theme" /> 189 <expand macro="theme" />
208 <expand macro="legend" /> 190 <expand macro="legend" />
218 <test> 200 <test>
219 <param name="input1" value="mtcars.txt" ftype="tabular" /> 201 <param name="input1" value="mtcars.txt" ftype="tabular" />
220 <param name="additional_output_format" value="pdf" /> 202 <param name="additional_output_format" value="pdf" />
221 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" /> 203 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" />
222 </test> 204 </test>
205 <!-- Test text options-->
206 <test>
207 <param name="input1" value="mtcars.txt" ftype="tabular" />
208 <section name="adv">
209 <conditional name="type_conditional">
210 <param name="type_options" value="points"/>
211 <conditional name="points">
212 <param name="pointoptions" value="default"/>
213 </conditional>
214 </conditional>
215 <conditional name="axis_text_customization">
216 <param name="axis_customization" value="defined"/>
217 <param name="color" value="red"/>
218 </conditional>
219 </section>
220 <param name="additional_output_format" value="pdf" />
221 <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" />
222 </test>
223 </tests> 223 </tests>
224 <help><![CDATA[ 224 <help><![CDATA[
225 This tool will generate a scatterplot representing data from two groups/conditions. 225 This tool will generate a scatterplot representing data from two groups/conditions.
226 226
227 The input data should be in tabular format and the user can determine which groups (columns) to plot. 227 The input data should be in tabular format and the user can determine which groups (columns) to plot.
228 228
229 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups". 229 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "advanced - plotting multiple groups".
230 230
231 Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user! 231 Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!
232 232
233 The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions" 233 The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "advanced - output dimensions"
234 ]]></help> 234 ]]></help>
235 <expand macro="citations"/> 235 <expand macro="citations"/>
236 </tool> 236 </tool>