Mercurial > repos > galaxyp > msi_spectra_plot

comparison msi_spectra_plots.xml @ 5:4f13aec6d8ff draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
author galaxyp
date Fri, 06 Jul 2018 14:14:41 -0400
parents 9eef2792afa4
children 2e0368a6bfe8
comparison
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4:9eef2792afa4 5:4f13aec6d8ff
1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.2"> 1 <tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.3">
2 <description> 2 <description>
3 mass spectrometry imaging mass spectra plots 3 mass spectrometry imaging mass spectra plots
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> 6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
32 library(Cardinal) 32 library(Cardinal)
33 library(gridExtra) 33 library(gridExtra)
34 library(ggplot2) 34 library(ggplot2)
35 library(scales) 35 library(scales)
36 36
37
37 #if $infile.ext == 'imzml' 38 #if $infile.ext == 'imzml'
38 msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") 39 #if str($processed_cond.processed_file) == "processed":
40 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
41 #else
42 msidata <- readImzML('infile', attach.only=TRUE)
43 #end if
39 #elif $infile.ext == 'analyze75' 44 #elif $infile.ext == 'analyze75'
40 msidata = readAnalyze('infile') 45 msidata = readAnalyze('infile', attach.only=TRUE)
41 #else 46 #else
42 load('infile.RData') 47 load('infile.RData')
43 #end if 48 #end if
44 49
45 ###################################### file properties in numbers ############## 50 ###################################### file properties in numbers ##############
56 maximumx = max(coord(msidata)[,1]) 61 maximumx = max(coord(msidata)[,1])
57 ## Range y coordinates 62 ## Range y coordinates
58 minimumy = min(coord(msidata)[,2]) 63 minimumy = min(coord(msidata)[,2])
59 maximumy = max(coord(msidata)[,2]) 64 maximumy = max(coord(msidata)[,2])
60 ## Range of intensities 65 ## Range of intensities
61 minint = round(min(spectra(msidata)[]), digits=2) 66 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
62 maxint = round(max(spectra(msidata)[]), digits=2) 67 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
63 medint = round(median(spectra(msidata)[]), digits=2) 68 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
64 ## Number of intensities > 0 69 ## Number of intensities > 0
65 npeaks= sum(spectra(msidata)[]>0) 70 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
66 ## Spectra multiplied with m/z (potential number of peaks) 71 ## Spectra multiplied with m/z (potential number of peaks)
67 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[]) 72 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
68 ## Percentage of intensities > 0 73 ## Percentage of intensities > 0
69 percpeaks = round(npeaks/numpeaks*100, digits=2) 74 percpeaks = round(npeaks/numpeaks*100, digits=2)
70 ## Number of empty TICs 75 ## Number of empty TICs
71 TICs = colSums(spectra(msidata)[]) 76 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
72 NumemptyTIC = sum(TICs == 0) 77 NumemptyTIC = sum(TICs == 0)
78
73 79
74 ## Processing informations 80 ## Processing informations
75 processinginfo = processingData(msidata) 81 processinginfo = processingData(msidata)
76 centroidedinfo = processinginfo@centroided 82 centroidedinfo = processinginfo@centroided
77 83
174 180
175 if (pixelisvalid == "TRUE"){ 181 if (pixelisvalid == "TRUE"){
176 print(pixelisvalid) 182 print(pixelisvalid)
177 183
178 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1), 184 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1),
179 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram", 185 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,
180 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy)) 186 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
181 187
182 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) 188 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
183 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth) 189 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
184 190
187 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) 193 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
188 194
189 ##################### IV) plot zoom-in mass spectrum ############### 195 ##################### IV) plot zoom-in mass spectrum ###############
190 196
191 #if $chosenpixel.zoomedplot: 197 #if $chosenpixel.zoomedplot:
198 iData(msidata) <- iData(msidata)[] ## getting back data on disk
199
192 #for $token in $chosenpixel.zoomedplot: 200 #for $token in $chosenpixel.zoomedplot:
193 201
194 minmasspixel = features(msidata, mz=$token.xlimmin) 202 minmasspixel = features(msidata, mz=$token.xlimmin)
195 maxmasspixel = features(msidata, mz=$token.xlimmax) 203 maxmasspixel = features(msidata, mz=$token.xlimmax)
196 204
202 }else{ 210 }else{
203 print("The pixel coordinates did not correspond to a real pixel")} 211 print("The pixel coordinates did not correspond to a real pixel")}
204 #end for 212 #end for
205 213
206 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file") 214 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
207
208 215
209 ############################# sample pixel ################################ 216 ############################# sample pixel ################################
210 ########################################################################### 217 ###########################################################################
211 218
212 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel': 219 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
258 ## print legend only for less than 10 samples 265 ## print legend only for less than 10 samples
259 if (length(levels(msidata\$combined_sample)) < 10){ 266 if (length(levels(msidata\$combined_sample)) < 10){
260 key_legend = TRUE 267 key_legend = TRUE
261 }else{key_legend = FALSE} 268 }else{key_legend = FALSE}
262 269
270 spectra(msidata) = is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
271
263 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE) 272 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$combined_sample, key=key_legend, col=hue_pal()(length(levels(msidata\$combined_sample))),superpose=TRUE)
264 }else{ 273 }else{
274 spectra(msidata) = is.na(spectra(msidata)[]) == 0 ## in case of NA values they will be set to zero
265 plot(msidata, pixel=1:ncol(msidata), key=TRUE)} 275 plot(msidata, pixel=1:ncol(msidata), key=TRUE)}
266 276
267 ##################### II) Sample: plot zoom-in mass spectrum ########## 277 ##################### II) Sample: plot zoom-in mass spectrum ##########
268 278
269 #if $pixel_conditional.zoomed_sample: 279 #if $pixel_conditional.zoomed_sample:
280 iData(msidata) <- iData(msidata)[] ## getting back data on disk
270 #for $token in $pixel_conditional.zoomed_sample: 281 #for $token in $pixel_conditional.zoomed_sample:
271 print("zoomed sample pixels") 282 print("zoomed sample pixels")
272 283
273 minmasspixel = features(msidata, mz=$token.xlimmin) 284 minmasspixel = features(msidata, mz=$token.xlimmin)
274 maxmasspixel = features(msidata, mz=$token.xlimmax) 285 maxmasspixel = features(msidata, mz=$token.xlimmax)
282 }else{ 293 }else{
283 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))} 294 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))}
284 295
285 #end for 296 #end for
286 #end if 297 #end if
298
287 if (!is.null(levels(msidata\$combined_sample))){ 299 if (!is.null(levels(msidata\$combined_sample))){
288 pixeldf = data.frame(table(msidata\$combined_sample)) 300 pixeldf = data.frame(table(msidata\$combined_sample))
289 }else{ 301 }else{
290 pixeldf = data.frame("$filename", ncol(msidata))} 302 pixeldf = data.frame("$filename", ncol(msidata))}
291 colnames(pixeldf) = c("sample name", "number of pixels") 303 colnames(pixeldf) = c("sample name", "number of pixels")
292 304
293 #end if 305 #end if
306
307
308 ############################# pixel table ######################################
309 ###############################################################################
310
294 311
295 ### overview table of pixels or samples: 312 ### overview table of pixels or samples:
296 plot(0,type='n',axes=FALSE,ann=FALSE) 313 plot(0,type='n',axes=FALSE,ann=FALSE)
297 title(main="Overview of chosen pixel:") 314 title(main="Overview of chosen pixel:")
298 315
325 ]]></configfile> 342 ]]></configfile>
326 </configfiles> 343 </configfiles>
327 <inputs> 344 <inputs>
328 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" 345 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
329 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> 346 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
330 <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> 347 <conditional name="processed_cond">
331 <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> 348 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
332 <option value="mz" >mz</option> 349 <option value="no_processed" selected="True">not a processed imzML</option>
333 <option value="ppm" selected="True" >ppm</option> 350 <option value="processed">processed imzML</option>
334 </param> 351 </param>
352 <when value="no_processed"/>
353 <when value="processed">
354 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
355 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
356 <option value="mz" >mz</option>
357 <option value="ppm" selected="True" >ppm</option>
358 </param>
359 </when>
360 </conditional>
335 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/> 361 <param name="filename" type="text" value="" label="Title" help="will appear in the pdf output. If nothing given it will take the dataset name"/>
336 <conditional name="pixel_conditional"> 362 <conditional name="pixel_conditional">
337 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or of all pixels of a sample"> 363 <param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or the average spectrum of all pixels of a sample">
338 <option value="single_pixel" selected="True">Single pixel</option> 364 <option value="single_pixel" selected="True">Single pixel</option>
339 <option value="sample_pixel">All pixels of a sample</option> 365 <option value="sample_pixel">Average spectrum for each sample</option>
340 </param> 366 </param>
341 <when value="single_pixel"> 367 <when value="single_pixel">
342 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20"> 368 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
343 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/> 369 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
344 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/> 370 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>