|
1
|
1 #TO ACCOMPANY ggplot_point.xml version 0.1.2
|
|
|
2 # Setup R error handling to go to stderr
|
|
|
3 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
|
|
|
4
|
|
|
5 # We need to not crash galaxy with an UTF8 error on German LC settings.
|
|
|
6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
|
|
|
7
|
|
|
8
|
|
|
9 # Import library
|
|
|
10 library("getopt")
|
|
|
11 library("ggplot2")
|
|
|
12 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
|
|
|
13 # Take in trailing command line arguments
|
|
|
14 args <- commandArgs(trailingOnly = TRUE)
|
|
|
15
|
|
|
16
|
|
|
17 # get options, using the spec as defined by the enclosed list.
|
|
|
18 # we read the options from the default: commandArgs(TRUE).
|
|
|
19 option_specification = matrix(c(
|
|
|
20 'input', 'i', 2, 'character',
|
|
|
21 'title', 't',2, 'character',
|
|
|
22 'size', 's', 2, 'double',
|
|
|
23 'xlab', 'x', 2, 'character',
|
|
|
24 'ylab', 'y', 2, 'character',
|
|
|
25 'xplot', 'z', 2, 'integer',
|
|
|
26 'yplot', 'j', 2, 'integer',
|
|
|
27 'xaxismin', 'e', 2, 'integer',
|
|
|
28 'xaxismax', 'f', 2, 'integer',
|
|
|
29 'yaxismin', 'g', 2, 'integer',
|
|
|
30 'yaxismax', 'h', 2, 'integer',
|
|
|
31 'alpha', 'a', 2, 'double',
|
|
|
32 'points', 'p', 2, 'character',
|
|
|
33 'theme', 'l', 2, 'character',
|
|
|
34 'scaling', 'b', 2, 'character',
|
|
|
35 'transform', 'w', 2, 'character',
|
|
|
36 'dim', 'k', 2, 'character',
|
|
|
37 'woutputdim', 'c', 2, 'integer',
|
|
|
38 'houtputdim', 'd', 2, 'integer',
|
|
|
39 'factor', 'n', 2, 'character',
|
|
|
40 'factorcol', 'm', 2, 'integer',
|
|
|
41 'colors', 'q', 2, 'character',
|
|
|
42 'colororder', 'r', 2, 'integer',
|
|
|
43 'pointcolor', 'u', 2, 'character',
|
|
|
44 'axistitlecust', 'v', 2, 'character',
|
|
|
45 'axistitlecolor', '1', 2, 'character',
|
|
|
46 'axistitlesize', '2', 2, 'integer',
|
|
|
47 'axistitleface', '3', 2, 'character',
|
|
|
48 'axistextcust', '4', 2, 'character',
|
|
|
49 'axistextcolor', '5', 2, 'character',
|
|
|
50 'axistextsize', '6', 2, 'integer',
|
|
|
51 'axistextface', '7', 2, 'character',
|
|
|
52 'plottitlecust', '8', 2, 'character',
|
|
|
53 'plottitlecolor', '9', 2, 'character',
|
|
|
54 'plottitlesize', '10', 2, 'integer',
|
|
|
55 'plottitleface', '11', 2, 'character',
|
|
|
56 'gridlinecust', '12', 2, 'character',
|
|
|
57 'output', 'o', 2, 'character'
|
|
|
58 ), byrow=TRUE, ncol=4);
|
|
|
59
|
|
|
60 # Parse options
|
|
|
61 options = getopt(option_specification);
|
|
|
62
|
|
|
63
|
|
|
64
|
|
|
65 # Print options to see what is going on
|
|
|
66 cat("\n input: ",options$input)
|
|
|
67 cat("\n title: ",options$title)
|
|
|
68 cat("\n xlab: ",options$xlab)
|
|
|
69 cat("\n ylab: ",options$ylab)
|
|
|
70 cat("\n points: ",options$points)
|
|
|
71 cat("\n theme: ",options$theme)
|
|
|
72 cat("\n scaling: ",options$scaling)
|
|
|
73 cat("\n transform: ",options$transform)
|
|
|
74
|
|
|
75
|
|
|
76
|
|
|
77 #Choose between automatically scaled x and y axis or user defined
|
|
|
78 if(options$scaling == "Automatic"){
|
|
|
79 gg_scalex = NULL
|
|
|
80 gg_scaley = NULL
|
|
|
81 } else {
|
|
|
82 gg_scalex = xlim(options$xaxismin,options$xaxismax)
|
|
|
83 gg_scaley = ylim(options$yaxismin,options$yaxismax)
|
|
|
84 cat("\n xaxismin: ",options$xaxismin)
|
|
|
85 cat("\n xaxismax: ",options$xaxismax)
|
|
|
86 cat("\n yaxismin: ",options$yaxismin)
|
|
|
87 cat("\n yaxismax: ",options$yaxismax)
|
|
|
88 }
|
|
|
89
|
|
|
90 # Choose theme for plot
|
|
|
91 if(options$theme == "bw"){
|
|
|
92 gg_theme = theme_bw()
|
|
|
93 } else {
|
|
|
94 gg_theme = NULL
|
|
|
95 }
|
|
|
96
|
|
|
97 #Choose dimensions of output pdf
|
|
|
98 if(options$dim == "Default"){
|
|
|
99 gg_width = 7
|
|
|
100 gg_height = 7
|
|
|
101 } else {
|
|
|
102 gg_width = options$woutputdim
|
|
|
103 gg_height = options$houtputdim
|
|
|
104 }
|
|
|
105
|
|
|
106 input <-read.table(options$input, check.names=TRUE, header=TRUE, row.names=NULL)
|
|
|
107
|
|
|
108 #renaming columns so ggplot can use them
|
|
|
109 names(input)[options$xplot] <- "xcol"
|
|
|
110 names(input)[options$yplot] <- "ycol"
|
|
|
111
|
|
|
112 #choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
|
|
|
113 if(options$factor == "Multiple"){
|
|
|
114 gg_facet = facet_wrap( ~ factor)
|
|
|
115 gg_factor = NULL
|
|
|
116 color_scale = NULL
|
|
|
117
|
|
|
118 if(options$points == "Default"){
|
|
|
119 gg_point = geom_point(size=1, alpha=1, gg_factor)
|
|
|
120 } else {
|
|
|
121 gg_point = geom_point(size=options$size, alpha=options$alpha, colour=options$pointcolor)
|
|
|
122 cat("\n size: ",options$size)
|
|
|
123 cat("\n alpha: ",options$alpha)
|
|
|
124 cat("\n pointcolor: ",options$pointcolor)
|
|
|
125 }
|
|
|
126
|
|
|
127 names(input)[options$factorcol] <- "factor"
|
|
|
128
|
|
|
129 cat("\n factor: ",options$factor)
|
|
|
130 cat("\n factorcol: ",options$factorcol)
|
|
|
131 } else if(options$factor == "Single"){
|
|
|
132 gg_facet = NULL
|
|
|
133 gg_factor = aes(colour=factor(factor))
|
|
|
134
|
|
|
135 if(options$points == "Default"){
|
|
|
136 gg_point = geom_point(size=1, alpha=1, gg_factor)
|
|
|
137 } else {
|
|
|
138 gg_point = geom_point(size=options$size, alpha=options$alpha, gg_factor)
|
|
|
139 cat("\n size: ",options$size)
|
|
|
140 cat("\n alpha: ",options$alpha)
|
|
|
141 cat("\n pointcolor: ",options$pointcolor)
|
|
|
142 }
|
|
|
143
|
|
|
144 if(options$colors == "Default"){
|
|
|
145 color_scale = scale_colour_hue(direction=options$colororder)
|
|
|
146 } else {
|
|
|
147 color_scale = scale_color_brewer(palette=options$colors, direction=options$colororder)
|
|
|
148 }
|
|
|
149
|
|
|
150 names(input)[options$factorcol] <- "factor"
|
|
|
151
|
|
|
152 cat("\n factor: ",options$factor)
|
|
|
153 cat("\n factorcol: ",options$factorcol)
|
|
|
154 cat("\n color_scale: ",options$colors)
|
|
|
155 cat("\n color_order: ",options$colororder)
|
|
|
156 } else{
|
|
|
157 gg_facet = NULL
|
|
|
158 gg_factor = NULL
|
|
|
159 color_scale = NULL
|
|
|
160
|
|
|
161 if(options$points == "Default"){
|
|
|
162 gg_point = geom_point(size=1, alpha=1, gg_factor)
|
|
|
163 } else {
|
|
|
164 gg_point = geom_point(size=options$size, alpha=options$alpha, colour=options$pointcolor)
|
|
|
165 cat("\n size: ",options$size)
|
|
|
166 cat("\n alpha: ",options$alpha)
|
|
|
167 cat("\n pointcolor: ",options$pointcolor)
|
|
|
168 }
|
|
|
169 }
|
|
|
170
|
|
|
171
|
|
|
172 #Selecting whether or not to log transform data
|
|
|
173 if(options$transform == "log2"){
|
|
|
174 input[, options$xplot] <- log2(input[options$xplot])
|
|
|
175 input[, options$yplot] <- log2(input[options$yplot])
|
|
|
176 }else if(options$transform == "log2plus1"){
|
|
|
177 input[, options$xplot] <- log2(input[options$xplot]+1)
|
|
|
178 input[, options$yplot] <- log2(input[options$yplot]+1)
|
|
|
179 }else if(options$transform == "log10"){
|
|
|
180 input[, options$xplot] <- log10(input[options$xplot])
|
|
|
181 input[, options$yplot] <- log10(input[options$yplot])
|
|
|
182 }else if(options$transform == "log10plus1"){
|
|
|
183 input[, options$xplot] <- log10(input[options$xplot]+1)
|
|
|
184 input[, options$yplot] <- log10(input[options$yplot]+1)
|
|
|
185 }else{
|
|
|
186 }
|
|
|
187
|
|
|
188
|
|
|
189 #axis label custization
|
|
|
190 if(options$axistitlecust == "Default"){
|
|
|
191 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
|
|
|
192 } else {
|
|
|
193 gg_axistitle = theme(axis.title = element_text(color = options$axistitlecolor, size = options$axistitlesize, face = options$axistitleface))
|
|
|
194 }
|
|
|
195
|
|
|
196
|
|
|
197 #axis text(tick) custization
|
|
|
198 if(options$axistextcust == "Default"){
|
|
|
199 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
|
|
|
200 } else {
|
|
|
201 gg_axistext = theme(axis.text = element_text(color = options$axistextcolor, size = options$axistextsize, face = options$axistextface))
|
|
|
202 }
|
|
|
203
|
|
|
204
|
|
|
205 #plot title custimization
|
|
|
206 if(options$plottitlecust == "Default"){
|
|
|
207 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
|
|
|
208 } else {
|
|
|
209 gg_plottitle = theme(plot.title = element_text(color = options$plottitlecolor, size = options$plottitlesize, face = options$plottitleface))
|
|
|
210 }
|
|
|
211
|
|
|
212 #grid line customization
|
|
|
213 if(options$gridlinecust == "Default"){
|
|
|
214 gg_gridline = NULL
|
|
|
215 } else if(options$gridlinecust == "hidemajor"){
|
|
|
216 gg_gridline = theme(panel.grid.major = element_blank())
|
|
|
217 } else if(options$gridlinecust == "hideminor"){
|
|
|
218 gg_gridline = theme(panel.grid.minor = element_blank())
|
|
|
219 } else if(options$gridlinecust == "hideboth"){
|
|
|
220 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
|
|
|
221 } else {
|
|
|
222 }
|
|
|
223
|
|
|
224
|
|
|
225 #this is the actual ggplot command to make the final plot(s)
|
|
|
226 ggplot(input, aes(xcol,ycol))+gg_point+gg_facet+
|
|
|
227 gg_theme+gg_scalex+gg_scaley+color_scale+ggtitle(options$title)+xlab(options$xlab)+ylab(options$ylab)+
|
|
|
228 gg_axistitle+gg_axistext+gg_plottitle+gg_gridline
|
|
|
229
|
|
|
230 ggsave(file=options$output, width=gg_width, height=gg_height)
|
