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comparison test-data/heatmap.txt @ 6:c3b54a4b7741 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:47 -0400
parents 78fcfc04fcfe
children
comparison
equal deleted inserted replaced
5:78fcfc04fcfe 6:c3b54a4b7741
1 > get_features <- function(myGenes, f="gene") {
2 + if (f == "isoforms")
3 + return(isoforms(myGenes))
4 + else if (f == "tss")
5 + return(TSS(myGenes))
6 + else if (f == "cds")
7 + return(CDS(myGenes))
8 + else
9 + return(myGenes)
10 + }
11 >
12 > ## Main Function ##
13 >
14 > library(argparse)
15 Loading required package: proto
16 >
17 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
18 >
19 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
20 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
21 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
22 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
23 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
24 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
25 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
26 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
27 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
28 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
29 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
30 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
31 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
32 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
33 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
34 > parser$add_argument('--features', dest='features', action="store", default="genes")
35 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
36 > parser$add_argument('--iter_max', dest='iter_max', action="store")
37 > parser$add_argument('--genes', dest='genes', action="append")
38 > parser$add_argument('--k', dest='k', action="store")
39 > parser$add_argument('--x', dest='x', action="store")
40 > parser$add_argument('--y', dest='y', action="store")
41 >
42 > args <- parser$parse_args()
43 >
44 > ## Load cummeRbund library
45 > library("cummeRbund")
46 Loading required package: BiocGenerics
47 Loading required package: methods
48 Loading required package: parallel
49
50 Attaching package: ‘BiocGenerics’
51
52 The following objects are masked from ‘package:parallel’:
53
54 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
55 clusterExport, clusterMap, parApply, parCapply, parLapply,
56 parLapplyLB, parRapply, parSapply, parSapplyLB
57
58 The following objects are masked from ‘package:stats’:
59
60 IQR, mad, xtabs
61
62 The following objects are masked from ‘package:base’:
63
64 anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
65 duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
66 is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
67 paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
68 Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
69 unique, unsplit, which, which.max, which.min
70
71 Loading required package: RSQLite
72 Loading required package: DBI
73 Loading required package: ggplot2
74 Loading required package: reshape2
75 Loading required package: fastcluster
76
77 Attaching package: ‘fastcluster’
78
79 The following object is masked from ‘package:stats’:
80
81 hclust
82
83 Loading required package: rtracklayer
84 Loading required package: GenomicRanges
85 Loading required package: stats4
86 Loading required package: S4Vectors
87
88 Attaching package: ‘S4Vectors’
89
90 The following objects are masked from ‘package:base’:
91
92 colMeans, colSums, expand.grid, rowMeans, rowSums
93
94 Loading required package: IRanges
95 Loading required package: GenomeInfoDb
96 Loading required package: Gviz
97 Loading required package: grid
98 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
99 by .GlobalEnv when processing object ‘plot.index’
100 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
101 by .GlobalEnv when processing object ‘plot.index’
102 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
103 by .GlobalEnv when processing object ‘plot.index’
104 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
105 by .GlobalEnv when processing object ‘plot.index’
106 Warning: namespace ‘ensembldb’ is not available and has been replaced
107 by .GlobalEnv when processing object ‘plot.index’
108 Warning: namespace ‘ensembldb’ is not available and has been replaced
109 by .GlobalEnv when processing object ‘plot.index’
110 Warning: namespace ‘ensembldb’ is not available and has been replaced
111 by .GlobalEnv when processing object ‘plot.index’
112 Warning: namespace ‘ensembldb’ is not available and has been replaced
113 by .GlobalEnv when processing object ‘plot.index’
114 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
115 by .GlobalEnv when processing object ‘plot.index’
116 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
117 by .GlobalEnv when processing object ‘plot.index’
118 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
119 by .GlobalEnv when processing object ‘plot.index’
120 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
121 by .GlobalEnv when processing object ‘plot.index’
122 Warning: namespace ‘ensembldb’ is not available and has been replaced
123 by .GlobalEnv when processing object ‘plot.index’
124 Warning: namespace ‘ensembldb’ is not available and has been replaced
125 by .GlobalEnv when processing object ‘plot.index’
126 Warning: namespace ‘ensembldb’ is not available and has been replaced
127 by .GlobalEnv when processing object ‘plot.index’
128 Warning: namespace ‘ensembldb’ is not available and has been replaced
129 by .GlobalEnv when processing object ‘plot.index’
130 Warning: namespace ‘ensembldb’ is not available and has been replaced
131 by .GlobalEnv when processing object ‘plot.index’
132 Warning: namespace ‘ensembldb’ is not available and has been replaced
133 by .GlobalEnv when processing object ‘plot.index’
134 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
135 by .GlobalEnv when processing object ‘plot.index’
136 Warning: namespace ‘ensembldb’ is not available and has been replaced
137 by .GlobalEnv when processing object ‘plot.index’
138 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
139 by .GlobalEnv when processing object ‘plot.index’
140 Warning: namespace ‘ensembldb’ is not available and has been replaced
141 by .GlobalEnv when processing object ‘plot.index’
142 Warning: namespace ‘ensembldb’ is not available and has been replaced
143 by .GlobalEnv when processing object ‘plot.index’
144 Warning: namespace ‘ensembldb’ is not available and has been replaced
145 by .GlobalEnv when processing object ‘plot.index’
146 Warning: namespace ‘ensembldb’ is not available and has been replaced
147 by .GlobalEnv when processing object ‘plot.index’
148 Warning: namespace ‘ensembldb’ is not available and has been replaced
149 by .GlobalEnv when processing object ‘plot.index’
150 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
151 by .GlobalEnv when processing object ‘plot.index’
152 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
153 by .GlobalEnv when processing object ‘plot.index’
154
155 Attaching package: ‘cummeRbund’
156
157 The following object is masked from ‘package:GenomicRanges’:
158
159 promoters
160
161 The following object is masked from ‘package:IRanges’:
162
163 promoters
164
165 The following object is masked from ‘package:BiocGenerics’:
166
167 conditions
168
169 >
170 > ## Initialize cuff object
171 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
172 >
173 > ## Print out info
174 > print(cuff)
175 CuffSet instance with:
176 2 samples
177 87 genes
178 90 isoforms
179 88 TSS
180 0 CDS
181 87 promoters
182 88 splicing
183 0 relCDS
184 > sink("cuffdb_info.txt")
185 > print(cuff)
186 > print("SAMPLES:")
187 > samples(cuff)
188 > print("REPLICATES:")
189 > replicates(cuff)
190 > print("FEATURES:")
191 > print(annotation(genes(cuff)))
192 > cat(annotation(genes(cuff))[[1]],sep=",")
193 > sink()
194 >
195 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
196 > tryCatch({
197 + if (args$plotType == 'density') {
198 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
199 + }
200 + else if (args$plotType == 'boxplot') {
201 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
202 + }
203 + else if (args$plotType == 'mds') {
204 + MDSplot(genes(cuff), replicates=args$replicates)
205 + }
206 + else if (args$plotType == 'pca') {
207 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
208 + }
209 + else if (args$plotType == 'dendrogram') {
210 + csDendro(genes(cuff), replicates=args$replicates)
211 + }
212 + else if (args$plotType == 'scatter') {
213 + if (args$gene_selector) {
214 + myGenes <- getGenes(cuff, args$genes)
215 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
216 + }
217 + else {
218 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
219 + }
220 + }
221 + else if (args$plotType == 'volcano') {
222 + if (args$gene_selector) {
223 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
224 + }
225 + else {
226 + myGenes <- genes(cuff)
227 + }
228 + csVolcano(myGenes, args$x, args$y)
229 + }
230 + else if (args$plotType == 'heatmap') {
231 + if (args$gene_selector) {
232 + myGenes <- getGenes(cuff, args$genes)
233 + }
234 + else {
235 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
236 + }
237 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
238 + }
239 + else if (args$plotType == 'cluster') {
240 + myGenes <- getGenes(cuff, args$genes)
241 + csCluster(get_features(myGenes, args$features), k=args$k)
242 + }
243 + else if (args$plotType == 'dispersion') {
244 + dispersionPlot(genes(cuff))
245 + }
246 + else if (args$plotType == 'fpkmSCV') {
247 + fpkmSCVPlot(genes(cuff))
248 + }
249 + else if (args$plotType == 'scatterMatrix') {
250 + csScatterMatrix(genes(cuff))
251 + }
252 + else if (args$plotType == 'expressionplot') {
253 + myGenes <- getGenes(cuff, args$genes)
254 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
255 + }
256 + else if (args$plotType == 'expressionbarplot') {
257 + myGeneId <- args$genes
258 + myGenes <- getGenes(cuff, myGeneId)
259 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
260 + }
261 + else if (args$plotType == 'mds') {
262 + MDSplot(genes(cuff),replicates=args$replicates)
263 + }
264 + else if (args$plotType == 'pca') {
265 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
266 + }
267 + else if (args$plotType == 'maplot') {
268 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
269 + }
270 + else if (args$plotType == 'genetrack') {
271 + myGene <- getGene(cuff, args$genes)
272 + plotTracks(makeGeneRegionTrack(myGene))
273 + }
274 + },error = function(e) {
275 + write(paste("Failed:", e, sep=" "), stderr())
276 + q("no", 1, TRUE)
277 + })
278 Getting gene information:
279 FPKM
280 Differential Expression Data
281 Annotation Data
282 Replicate FPKMs
283 Counts
284 Getting isoforms information:
285 FPKM
286 Differential Expression Data
287 Annotation Data
288 Replicate FPKMs
289 Counts
290 Getting CDS information:
291 FPKM
292 Differential Expression Data
293 Annotation Data
294 Replicate FPKMs
295 Counts
296 Getting TSS information:
297 FPKM
298 Differential Expression Data
299 Annotation Data
300 Replicate FPKMs
301 Counts
302 Getting promoter information:
303 distData
304 Getting splicing information:
305 distData
306 Getting relCDS information:
307 distData
308 Using tracking_id, sample_name as id variables
309 No id variables; using all as measure variables
310 > devname = dev.off()
311 >