Mercurial > repos > iuc > ggplot2_point

comparison ggplot_point.xml @ 4:52b8083a6159 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
author iuc
date Sun, 24 Mar 2019 13:21:18 -0400
parents 9a482995958c
children 9cec81e1b90e
comparison
equal deleted inserted replaced
3:46f91106439b 4:52b8083a6159
1 <tool id="ggplot2_point" name="Scatterplot w ggplot2" version="@VERSION@+galaxy0"> 1 <tool id="ggplot2_point" name="Scatterplot w ggplot2" version="@VERSION@+galaxy1">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements"> 5 <expand macro="requirements">
6 <requirement type="package" version="1.2.1">r-svglite</requirement> 6 <requirement type="package" version="1.2.1">r-svglite</requirement>
33 gg_facet = facet_wrap( ~ factor) 33 gg_facet = facet_wrap( ~ factor)
34 gg_factor = NULL 34 gg_factor = NULL
35 color_scale = NULL 35 color_scale = NULL
36 #if $adv.points.pointoptions == "Default" 36 #if $adv.points.pointoptions == "Default"
37 gg_point = geom_point(size=1, alpha=1, gg_factor) 37 gg_point = geom_point(size=1, alpha=1, gg_factor)
38 gg_line = geom_line(size=1, alpha=1, gg_factor)
38 #else 39 #else
39 gg_point = geom_point(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor') 40 gg_point = geom_point(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
41 gg_line = geom_line(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
40 #end if 42 #end if
41 43
42 names(input)[$adv.factor.factorcol] <- "factor" 44 names(input)[$adv.factor.factorcol] <- "factor"
43 45
44 #elif $adv.factor.factoring == "Single" 46 #elif $adv.factor.factoring == "Single"
45 gg_facet = NULL 47 gg_facet = NULL
46 gg_factor = aes(colour=factor(factor)) 48 gg_factor = aes(colour=factor(factor))
47 49
48 #if $adv.points.pointoptions == "default" 50 #if $adv.points.pointoptions == "default"
49 gg_point = geom_point(size=1, alpha=1, gg_factor) 51 gg_point = geom_point(size=1, alpha=1, gg_factor)
52 gg_line = geom_line(size=1, alpha=1, gg_factor)
50 #else 53 #else
51 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor) 54 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
55 gg_line = geom_line(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
52 #end if 56 #end if
53 57
54 #if $adv.colors == "Default" 58 #if $adv.factor.colororder == 1
55 color_scale = scale_colour_hue(direction='$adv.factor.colororder') 59 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
56 #else 60 #else
57 color_scale = scale_color_brewer(palette='$adv.colors', direction='$adv.factor.colororder') 61 color_scale = scale_color_brewer(palette='$adv.factor.colors', direction='$adv.factor.colororder')
58 #end if 62 #end if
59 63
60 names(input)[$adv.factor.factorcol] <- "factor" 64 names(input)[$adv.factor.factorcol] <- "factor"
61 #else 65 #else
62 gg_facet = NULL 66 gg_facet = NULL
63 gg_factor = NULL 67 gg_factor = NULL
64 color_scale = NULL 68 color_scale = NULL
65 69
66 #if $adv.points.pointoptions == "default" 70 #if $adv.points.pointoptions == "default"
67 gg_point = geom_point(size=1, alpha=1, gg_factor) 71 gg_point = geom_point(size=1, alpha=1, gg_factor)
72 gg_line = geom_line(size=1, alpha=1, gg_factor)
68 #else 73 #else
69 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor') 74 gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
75 gg_line = geom_line(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
70 #end if 76 #end if
71 #end if 77 #end if
72 78
73 @TRANSFORM@ 79 @TRANSFORM@
74 80
102 gg_gridline = theme(panel.grid.minor = element_blank()) 108 gg_gridline = theme(panel.grid.minor = element_blank())
103 #elif $adv.gridlinecust == "hideboth" 109 #elif $adv.gridlinecust == "hideboth"
104 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank()) 110 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
105 #end if 111 #end if
106 112
113 ## choose between graph types (points/lines/both)
114 #if $adv.type == "points"
115 gg_line = NULL
116 #elif $adv.type == "lines"
117 gg_point = NULL
118 #end if
119
107 #this is the actual ggplot command to make the final plot(s) 120 #this is the actual ggplot command to make the final plot(s)
108 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_facet + 121 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
109 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+ 122 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
110 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline 123 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
111 124
112 @SAVE_OUTPUT@ 125 @SAVE_OUTPUT@
113 ]]></configfile> 126 ]]></configfile>
118 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" /> 131 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />
119 132
120 <expand macro="title" /> 133 <expand macro="title" />
121 <expand macro="xy_lab" /> 134 <expand macro="xy_lab" />
122 <section name="adv" title="Advanced Options" expanded="false"> 135 <section name="adv" title="Advanced Options" expanded="false">
136 <param name="type" type="select" label="Type of plot" >
137 <option value="points">Points only (default)</option>
138 <option value="lines">Lines only </option>
139 <option value="pointslines">Points and Lines</option>
140 </param>
123 <conditional name="points"> 141 <conditional name="points">
124 <param name="pointoptions" type="select" label="Data point options"> 142 <param name="pointoptions" type="select" label="Data point options">
125 <option value="default" selected="true">Default</option> 143 <option value="default" selected="true">Default</option>
126 <option value="defined">User defined point options</option> 144 <option value="defined">User defined point options</option>
127 </param> 145 </param>