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comparison spectra_plots.xml @ 7:64ea4507e0bd draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
author galaxyp
date Thu, 23 Apr 2020 08:05:19 -0400
parents 9b6b86e771c2
children 0b7e00e5b9d2
comparison
equal deleted inserted replaced
6:043f9c91f686 7:64ea4507e0bd
1 <tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.3"> 1 <tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0">
2 <description> 2 <description>
3 mass spectrometry imaging mass spectra plots 3 mass spectrometry imaging mass spectra plots
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="3.0">r-ggplot2</requirement> 9 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
10 <requirement type="package" version="2.3">r-gridextra</requirement> 10 <requirement type="package" version="2.3">r-gridextra</requirement>
11 <requirement type="package" version="1.0.0">r-scales</requirement> 11 <requirement type="package" version="1.0.0">r-scales</requirement>
12 </expand> 12 </expand>
13 <command detect_errors="exit_code"> 13 <command detect_errors="exit_code">
14 <![CDATA[ 14 <![CDATA[
26 library(gridExtra) 26 library(gridExtra)
27 library(ggplot2) 27 library(ggplot2)
28 library(scales) 28 library(scales)
29 29
30 30
31 @READING_MSIDATA@ 31 @READING_MSIDATA_FULLY_COMPATIBLE@
32 32
33 @DATA_PROPERTIES@ 33 @DATA_PROPERTIES@
34 34
35 35
36 ######################################## PDF ################################### 36 ######################################## PDF ###################################
49 ############################# I) numbers ###################################### 49 ############################# I) numbers ######################################
50 ############################################################################### 50 ###############################################################################
51 51
52 grid.table(property_df, rows= NULL) 52 grid.table(property_df, rows= NULL)
53 53
54 ## set NA to 0 otherwise plot function will not work
55
56 #if str($processed_cond.processed_file) == "processed":
57 ##processed file needs to be converted into matrix to be able to replace NAs
58 iData(msidata) <- iData(msidata)[]
59 #end if
60
61 spectra(msidata)[is.na(spectra(msidata))] = 0
62
63 ## run only if mz and pixels are > 0 54 ## run only if mz and pixels are > 0
64 55
65 if (ncol(msidata)>0 & nrow(msidata) >0){ 56 if (ncol(msidata)>0 & nrow(msidata) >0){
66 57
67 pixeldf = data.frame(matrix(ncol = 2, nrow=0)) 58 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
68 59
69 ############################# single pixel ################################ 60 ############################# single pixel ################################
70 ########################################################################### 61 ###########################################################################
71 62
72 #if str( $pixel_conditional.pixel_type) == 'single_pixel': 63 #if str( $pixel_conditional.pixel_type) == 'tabular_pixel':
73 print("single_pixel") 64 print("tabular_pixel")
74 65
75 #for $chosenpixel in $pixel_conditional.repeatpixel: 66 ## read and extract x,y, optional annotation information
76 67 spectra_tabular = read.delim("$pixel_conditional.pixel_file", header = $pixel_conditional.tabular_pixel_header, stringsAsFactors = FALSE)
77 pixelname = paste0("x = ", $chosenpixel.inputx,", ", "y = ", $chosenpixel.inputy) 68
78 69 #if $pixel_conditional.column_pixel_annotation:
79 70
80 71 spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.column_pixel_annotation)]
81 input_pixels = paste($chosenpixel.inputx, $chosenpixel.inputy, sep="_") 72 colnames(spectra_input) = c("x", "y", "annotation")
82 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_") 73
83 74 input_pixels = paste(spectra_input[,1], spectra_input[,2], sep="_")
84 pixelisvalid = as.character(input_pixels %in% dataset_pixels) 75 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
85 76 pixelsofinterest = dataset_pixels %in% input_pixels
86 77 msidata = msidata[,pixelsofinterest]
87 78
88 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid)) 79 ## merge with coordinate information of msidata
89 80 msidata_coordinates = data.frame(coord(msidata)\$x, coord(msidata)\$y, c(1:ncol(msidata)))
90 ############################# II) control image #################### 81 colnames(msidata_coordinates) = c("x", "y", "pixel_index")
91 82 merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)
92 if (pixelisvalid == "TRUE"){ 83 merged_annotation[is.na(merged_annotation)] = "NA"
93 84 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
94 image(msidata, mz=$chosenpixel.inputmz, ylim = c(maximumy+(0.2*maximumy),minimumy-1), 85 msidata\$annotation = as.factor(merged_annotation[,4])
95 colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton,
96 main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
97
98 abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
99 abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
100
101 ##################### III) plot full mass spectrum #################
102
103 plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), main="Mass spectrum of full m/z range")
104
105 ##################### IV) plot zoom-in mass spectrum ###############
106
107 #if $chosenpixel.zoomedplot:
108
109 #for $token in $chosenpixel.zoomedplot:
110
111 minmasspixel = features(msidata, mz=$token.xlimmin)
112 maxmasspixel = features(msidata, mz=$token.xlimmax)
113
114 plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
115 xlim= c($token.xlimmin,$token.xlimmax))
116
117 #end for
118 #end if
119 }else{
120 print("The pixel coordinates did not correspond to a real pixel")}
121 #end for
122
123 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
124
125 ############################# sample pixel ################################
126 ###########################################################################
127
128 #elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
129 print("sample pixels")
130
131 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
132
133 #if str($pixel_conditional.tabular_annotation.load_annotation) == 'yes_annotation':
134
135 ## read and extract x,y,annotation information
136 input_tabular = read.delim("$pixel_conditional.tabular_annotation.annotation_file", header = $pixel_conditional.tabular_annotation.tabular_header, stringsAsFactors = FALSE)
137 annotation_input = input_tabular[,c($pixel_conditional.tabular_annotation.column_x, $pixel_conditional.tabular_annotation.column_y, $pixel_conditional.tabular_annotation.column_names)]
138 colnames(annotation_input) = c("x", "y", "annotation")
139
140 ## merge with coordinate information of msidata
141 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
142 colnames(msidata_coordinates)[3] = "pixel_index"
143 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
144 merged_annotation[is.na(merged_annotation)] = "NA"
145 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
146 msidata\$annotation = as.factor(merged_annotation[,4])
147
148 #end if
149
150 ##################### I) Sample: plot full mass spectrum ##############
151
152 ## coloured plot with mean over all spectra with the same annotation, if no annotation is provided all pixels are considered as one sample
153
154 if (!is.null(levels(msidata\$annotation))){
155 print("annotated samples")
156 86
157 ## overview plot over annotated samples 87 ## overview plot over annotated samples
158 number_combined = length(levels(msidata\$annotation)) 88 number_combined = length(levels(msidata\$annotation))
159 89
160 ## the more annotation groups a file has the smaller will be the legend 90 ## the more annotation groups a file has the smaller will be the legend
168 legend_size = 7 98 legend_size = 7
169 }else{ 99 }else{
170 legend_size = 6 100 legend_size = 6
171 } 101 }
172 102
173 position_df = cbind(coord(msidata)[,1:2], as.factor(msidata\$annotation)) 103 position_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, as.factor(msidata\$annotation))
174 colnames(position_df)[3] = "sample_name" 104 colnames(position_df) = c("x", "y", "sample_name")
175 105
176 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+ 106 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
177 geom_tile(height = 1, width=1)+ 107 geom_tile(height = 1, width=1)+
178 coord_fixed()+ 108 coord_fixed()+
179 ggtitle("Spatial orientation of pixel annotations")+ 109 ggtitle("Spatial orientation of annotations")+
180 theme_bw()+ 110 theme_bw()+
181 theme(plot.title = element_text(hjust = 0.5))+ 111 theme(plot.title = element_text(hjust = 0.5))+
182 theme(text=element_text(family="ArialMT", face="bold", size=12))+ 112 theme(text=element_text(family="ArialMT", face="bold", size=12))+
183 theme(legend.position="bottom",legend.direction="vertical")+ 113 theme(legend.position="bottom",legend.direction="vertical")+
184 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+ 114 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+
196 ## print legend only for less than 10 samples 126 ## print legend only for less than 10 samples
197 if (length(levels(msidata\$annotation)) < 10){ 127 if (length(levels(msidata\$annotation)) < 10){
198 key_legend = TRUE 128 key_legend = TRUE
199 }else{key_legend = FALSE} 129 }else{key_legend = FALSE}
200 130
201 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, main="Average mass spectrum of full m/z range") 131 #if $fullmz:
202 }else{ 132 ## plot single tabular mz, average per annotation
203 plot(msidata, pixel=1:ncol(msidata), key=TRUE, main="Average mass spectrum of full m/z range")} 133 print(plot(msidata, run="infile", pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, strip=FALSE, grid=$grid_variable), main="Average spectrum per group")
134 #end if
135
136 pixeldf = data.frame(table(msidata\$annotation))
137 colnames(pixeldf) = c("sample name", "number of pixels")
138
139
140 ##################### II) Sample: plot zoom-in mass spectrum ##########
141
142 #if str($mz_range.mz_range_options) == "manual_mz":
143
144 #for $token in $mz_range.zoomed_sample:
145
146
147 minmasspixel = tryCatch(
148 {
149 features(msidata, mz=$token.xlimmin)
150 },
151 warning=function(cond) {
152 ## if xlimmin is outside mz range, use min mz value
153 return(features(msidata, mz=min(mz(msidata))))
154 }
155 )
156
157 maxmasspixel = tryCatch(
158 {
159 features(msidata, mz=$token.xlimmax)
160 },
161 warning=function(cond) {
162 ## if xlimax is outside mz range, use max mz value
163 return(features(msidata, mz=max(mz(msidata))))
164 }
165 )
166
167 ## plot single tabular mz, average per annotation, manual zoom
168 print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE,
169 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable,
170 key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE, main="Average spectrum per group"))
171 #end for
172
173 #elif str($mz_range.mz_range_options) == "tabular_mz":
174
175 input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
176 input_mz_features = input_mz[,c($mz_range.column_mz)]
177 for (feature_count in input_mz_features){
178
179 if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){
180
181 xlimmin = feature_count-$mz_range.minus_mz_tab
182 xlimmax = feature_count+$mz_range.plus_mz_tab
183
184 minmasspixel = features(msidata, mz=xlimmin)
185 maxmasspixel = features(msidata, mz=xlimmax)
186
187 ## plot single tabular mz, average per annotation, tabular zoom
188 print(plot(msidata[minmasspixel:maxmasspixel,], run="infile", strip=FALSE, main="Average spectrum per group",
189 xlim= c(xlimmin,xlimmax),pixel.groups=msidata\$annotation, grid = $grid_variable,
190 key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE))
191 }
192 }
193
194 #end if
195
196 #elif str($pixel_conditional.column_pixel_annotation)== "None":
197
198 spectra_tabular = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y)]
199 colnames(spectra_tabular) = c("x", "y")
200
201 dataset_pixels = data.frame(coord(msidata)\$x, coord(msidata)\$y)
202 colnames(dataset_pixels) = c("x", "y")
203 spectra_input = merge(dataset_pixels, spectra_tabular, by=c("x", "y"))
204 false_input = merge(spectra_tabular, spectra_input, by=c("x", "y"))
205
206 ## for loop for every valid spectrum (pixel)
207 for (pixel_count in 1:nrow(spectra_input)){
208
209 x_coord = spectra_input[pixel_count,1]
210 y_coord = spectra_input[pixel_count,2]
211
212
213 ##################### I) Sample: plot full mass spectrum ##############
214
215 #if $fullmz:
216 ## plot full mz for single tabular mz
217 print(plot(msidata, coord=list(x=x_coord, y=y_coord), key=TRUE, grid = $grid_variable))
218 #end if
219
220 pixelname = paste0("x = ", x_coord,", ", "y = ", y_coord)
221
222 input_pixels = paste(x_coord, y_coord, sep="_")
223 dataset_pixels = paste(coord(msidata)\$x, coord(msidata)\$y, sep="_")
224 pixelisvalid = as.character(input_pixels %in% dataset_pixels)
225
226 pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
227
228
229 ##################### II) Sample: plot zoom-in mass spectrum ##########
230
231 #if str($mz_range.mz_range_options) == "manual_mz":
232 #for $token in $mz_range.zoomed_sample:
233
234 minmasspixel = tryCatch(
235 {
236 features(msidata, mz=$token.xlimmin)
237 },
238 warning=function(cond) {
239 ## if xlimmin is outside mz range, use min mz value
240 return(features(msidata, mz=min(mz(msidata))))
241 }
242 )
243
244 maxmasspixel = tryCatch(
245 {
246 features(msidata, mz=$token.xlimmax)
247 },
248 warning=function(cond) {
249 ## if xlimax is outside mz range, use max mz value
250 return(features(msidata, mz=max(mz(msidata))))
251 }
252 )
253
254 ## same min and max not possible for plot
255 if (minmasspixel == maxmasspixel){
256 if (maxmasspixel == nrow(msidata)){
257 minmasspixel = minmasspixel-1
258 }else{
259 maxmasspixel = maxmasspixel+1
260 }
261 }
262
263 ## print single tabular mz; manual zoom
264 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))
265
266 #end for
267
268 #elif str($mz_range.mz_range_options) == "tabular_mz":
269
270 input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
271 input_mz_features = input_mz[,c($mz_range.column_mz)]
272 for (feature_count in input_mz_features){
273
274 if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){
275
276 xlimmin = feature_count-$mz_range.minus_mz_tab
277 xlimmax = feature_count+$mz_range.plus_mz_tab
278
279 minmasspixel = tryCatch(
280 {
281 features(msidata, mz=xlimmin)
282 },
283 warning=function(cond) {
284 ## if xlimmin is outside mz range, use min mz value
285 return(features(msidata, mz=min(mz(msidata))))
286 }
287 )
288
289 maxmasspixel = tryCatch(
290 {
291 maxmasspixel = features(msidata, mz=xlimmax)
292 },
293 warning=function(cond) {
294 ## if xlimax is outside mz range, use max mz value
295 return(features(msidata, mz=max(mz(msidata))))
296 }
297 )
298
299 ## same min and max not possible for plot
300 if (minmasspixel == maxmasspixel){
301 if (maxmasspixel == nrow(msidata)){
302 minmasspixel = minmasspixel-1
303 }else{
304 maxmasspixel = maxmasspixel+1
305 }
306 }
307
308 ## print single tabular mz; tabular zoom
309 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, coord=list(x=x_coord, y=y_coord), key=TRUE, xlim= c(xlimmin,xlimmax)))
310 }
311 }
312
313 #end if
314
315 }
316
317 colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
318
319 #end if
320
321
322 ############################# all pixel ################################
323 ###########################################################################
324
325 #elif str( $pixel_conditional.pixel_type) == 'all_pixel':
326 print("all pixels")
327
328 ##################### I) Sample: plot full mass spectrum ##############
329
330 #if $fullmz:
331
332 print(plot(msidata, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", grid = $grid_variable))
333 #end if
204 334
205 ##################### II) Sample: plot zoom-in mass spectrum ########## 335 ##################### II) Sample: plot zoom-in mass spectrum ##########
206 336
207 #if $pixel_conditional.zoomed_sample: 337 #if str($mz_range.mz_range_options) == "manual_mz":
208 #for $token in $pixel_conditional.zoomed_sample: 338 #for $token in $mz_range.zoomed_sample:
209 print("zoomed sample pixels") 339
210 340 minmasspixel = tryCatch(
211 minmasspixel = features(msidata, mz=$token.xlimmin) 341 {
212 maxmasspixel = features(msidata, mz=$token.xlimmax) 342 features(msidata, mz=$token.xlimmin)
213 343 },
214 ## coloured plot with mean over all spectra for annotation group, otherwise only 1 black plot 344 warning=function(cond) {
215 if (!is.null(levels(msidata\$annotation))){ 345 ## if xlimmin is outside mz range, use min mz value
216 print("annotation samples") 346 return(features(msidata, mz=min(mz(msidata))))
217 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), 347 }
218 xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=msidata\$annotation, 348 )
219 key=key_legend,col=hue_pal()(length(levels(msidata\$annotation))), superpose=TRUE) 349
220 }else{ 350 maxmasspixel = tryCatch(
221 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata), key=TRUE, xlim= c($token.xlimmin,$token.xlimmax))} 351 {
352 features(msidata, mz=$token.xlimmax)
353 },
354 warning=function(cond) {
355 ## if xlimax is outside mz range, use max mz value
356 return(features(msidata, mz=max(mz(msidata))))
357 }
358 )
359
360 ## same min and max not possible for plot
361 if (minmasspixel == maxmasspixel){
362 if (maxmasspixel == nrow(msidata)){
363 minmasspixel = minmasspixel-1
364 }else{
365 maxmasspixel = maxmasspixel+1
366 }
367 }
368
369 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, main="Average spectrum", run = "infile", strip=FALSE, key=TRUE, xlim= c($token.xlimmin,$token.xlimmax)))
222 370
223 #end for 371 #end for
372
373 #elif str($mz_range.mz_range_options) == "tabular_mz":
374
375 input_mz = read.delim("$mz_range.mz_file", header = $mz_range.tabular_header, stringsAsFactors = FALSE)
376 input_mz_features = input_mz[,c($mz_range.column_mz)]
377 for (feature_count in input_mz_features){
378
379 if (feature_count>min(mz(msidata))&feature_count<max(mz(msidata))){
380
381 xlimmin = feature_count-$mz_range.minus_mz_tab
382 xlimmax = feature_count+$mz_range.plus_mz_tab
383
384 minmasspixel = tryCatch(
385 {
386 features(msidata, mz=xlimmin)
387 },
388 warning=function(cond) {
389 ## if xlimmin is outside mz range, use min mz value
390 return(features(msidata, mz=min(mz(msidata))))
391 }
392 )
393
394 maxmasspixel = tryCatch(
395 {
396 maxmasspixel = features(msidata, mz=xlimmax)
397 },
398 warning=function(cond) {
399 ## if xlimax is outside mz range, use max mz value
400 return(features(msidata, mz=max(mz(msidata))))
401 }
402 )
403
404 print(plot(msidata[minmasspixel:maxmasspixel,], grid = $grid_variable, run="infile", key=TRUE, strip=FALSE, main="Average spectrum", xlim= c(xlimmin,xlimmax)))
405 }
406 }
407
408
224 #end if 409 #end if
225 410
226 if (!is.null(levels(msidata\$annotation))){ 411 pixeldf = data.frame("$filename", ncol(msidata))
227 pixeldf = data.frame(table(msidata\$annotation)) 412 colnames(pixeldf) = c("sample name", "number of pixels")
228 }else{
229 pixeldf = data.frame("$filename", ncol(msidata))}
230 colnames(pixeldf) = c("sample name", "number of pixels")
231 413
232 #end if 414 #end if
233 415
234 416
235 ############################# pixel table ###################################### 417 ############################# pixel table ######################################
272 </configfiles> 454 </configfiles>
273 <inputs> 455 <inputs>
274 <expand macro="reading_msidata"/> 456 <expand macro="reading_msidata"/>
275 <expand macro="pdf_filename"/> 457 <expand macro="pdf_filename"/>
276 <conditional name="pixel_conditional"> 458 <conditional name="pixel_conditional">
277 <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"> 459 <param name="pixel_type" type="select" label="Choose spectra (pixel)">
278 <option value="single_pixel" selected="True">Single pixel</option> 460 <option value="all_pixel" selected="True" >All spectra</option>
279 <option value="sample_pixel">Average spectrum for each sample</option> 461 <option value="tabular_pixel">Single spectra</option>
280 </param> 462 </param>
281 <when value="single_pixel"> 463 <when value="tabular_pixel">
282 <repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20"> 464 <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"
283 <param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/> 465 help="Two or three columns: x values, y values, optionally annotations"/>
284 <param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/> 466 <param name="column_pixel_x" data_ref="pixel_file" label="Column with x values" type="data_column"/>
285 <param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, define m/z here" help="m/z will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/> 467 <param name="column_pixel_y" data_ref="pixel_file" label="Column with y values" type="data_column"/>
286 <param name="plusminusinDalton" value="0.25" type="float" label="m/z range for this m/z value" help="plusminus m/z window "/> 468 <param name="column_pixel_annotation" data_ref="pixel_file" optional="True" label="Column with annotations" type="data_column"/>
287 <param name="inputcolour" type="select" label="Select the colour for the lines at x and y position"> 469 <param name="tabular_pixel_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
288 <option value="white" selected="True">white</option>
289 <option value="black">black</option>
290 <option value="grey">grey</option>
291 <option value="blue">blue</option>
292 <option value="red">red</option>
293 <option value="green">green</option>
294 </param>
295 <param name="inputtype" type="select" label="Select the line type for the lines at x and y position">
296 <option value="solid" selected="True">solid</option>
297 <option value="dashed">dashed</option>
298 <option value="dotted">dotted</option>
299 <option value="longdash">longdash</option>
300 </param>
301 <param name="inputwidth" type="integer" value="2" label="Select the width of the lines at x and y position"/>
302 <repeat name="zoomedplot" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50">
303 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/>
304 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/>
305 </repeat>
306 </repeat>
307 </when> 470 </when>
308 <when value="sample_pixel"> 471 <when value="all_pixel">
309 <conditional name="tabular_annotation"> 472 </when>
310 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for spectra plots"> 473 </conditional>
311 <option value="no_annotation" selected="True">pixels belong into one group only</option> 474 <param name="fullmz" type="boolean" label="Plot complete m/z range" checked="True" truevalue="TRUE" falsevalue="FALSE"/>
312 <option value="yes_annotation">group pixels according to annotations</option> 475 <conditional name="mz_range">
313 </param> 476 <param name="mz_range_options" type="select" label="zoomed in m/z range">
314 <when value="yes_annotation"> 477 <option value="none_mz" selected="True">no m/z range</option>
315 <expand macro="reading_pixel_annotations"/> 478 <option value="manual_mz" >Manual input</option>
316 </when> 479 <option value="tabular_mz">Tabular file</option>
317 <when value="no_annotation"/> 480 </param>
318 </conditional> 481 <when value="none_mz"/>
319 <repeat name="zoomed_sample" title="Zoomed in plots with m/z min and m/z max to define the plot window" min="0" max="50"> 482 <when value="tabular_mz">
320 <param name="xlimmin" type="integer" value="" label="lower m/z boundary for plotting window" help="minimum m/z for zoomed in window"/> 483 <param name="minus_mz_tab" type="float" value="" label="m/z value to subtract from m/z values in tabular file = lower m/z boundary"/>
321 <param name="xlimmax" type="integer" value="" label="upper m/z boundary for plotting window" help="maximum m/z for zoomed in window"/> 484 <param name="plus_mz_tab" type="float" value="" label="m/z value to add to m/z values in tabular file = upper m/z boundary"/>
485 <param name="mz_file" type="data" format="tabular" label="Load tabular file with m/z values"/>
486 <param name="column_mz" data_ref="mz_file" label="Column with mz values" type="data_column"/>
487 <param name="tabular_header" type="boolean" label="Tabular files contain a header line" truevalue="TRUE" falsevalue="FALSE"/>
488 </when>
489 <when value="manual_mz">
490 <repeat name="zoomed_sample" title="Define min m/z and max m/z for the plotting window" min="1">
491 <param name="xlimmin" type="float" value="" label="lower m/z boundary for plotting window"/>
492 <param name="xlimmax" type="float" value="" label="upper m/z boundary for plotting window"/>
322 </repeat> 493 </repeat>
323 </when> 494 </when>
324 </conditional> 495 </conditional>
496 <param name="grid_variable" type="boolean" label="Add grid to plot" truevalue="TRUE" falsevalue="FALSE"/>
325 </inputs> 497 </inputs>
326 <outputs> 498 <outputs>
327 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}:results"/> 499 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label="${tool.name} on ${on_string}:results"/>
328 </outputs> 500 </outputs>
329 <tests> 501 <tests>
330 <test> 502 <test>
331 <expand macro="infile_imzml"/> 503 <expand macro="infile_imzml"/>
332 <conditional name="pixel_conditional"> 504 <conditional name="pixel_conditional">
333 <param name="pixel_type" value="single_pixel"/> 505 <param name="pixel_type" value="tabular_pixel"/>
334 <repeat name="repeatpixel"> 506 <param name="pixel_file" value="spectra_1_pixel.tabular"/>
335 <param name="plusminusinDalton" value="0.25"/> 507 <param name="column_pixel_x" value="1"/>
336 <param name="inputx" value="3"/> 508 <param name="column_pixel_y" value="2"/>
337 <param name="inputy" value="3"/> 509 <param name="tabular_pixel_header" value="FALSE"/>
338 <repeat name="zoomedplot"> 510 </conditional>
339 <param name="xlimmin" value="310"/> 511 <param name="fullmz" value="TRUE"/>
340 <param name="xlimmax" value="320"/> 512 <conditional name="mz_range">
341 </repeat> 513 <param name="mz_range_options" value="manual_mz"/>
342 <repeat name="zoomedplot"> 514 <repeat name="zoomed_sample">
343 <param name="xlimmin" value="350"/> 515 <param name="xlimmin" value="310"/>
344 <param name="xlimmax" value="400"/> 516 <param name="xlimmax" value="320"/>
345 </repeat> 517 </repeat>
346 <repeat name="zoomedplot"> 518 <repeat name="zoomed_sample">
347 <param name="xlimmin" value="400"/> 519 <param name="xlimmin" value="350"/>
348 <param name="xlimmax" value="420"/> 520 <param name="xlimmax" value="400"/>
349 </repeat> 521 </repeat>
350 </repeat> 522 <repeat name="zoomed_sample">
351 <repeat name="repeatpixel"> 523 <param name="xlimmin" value="360"/>
352 <param name="plusminusinDalton" value="0.25"/> 524 <param name="xlimmax" value="360.8"/>
353 <param name="inputx" value="2"/>
354 <param name="inputy" value="2"/>
355 </repeat>
356 <repeat name="repeatpixel">
357 <param name="plusminusinDalton" value="0.25"/>
358 <param name="inputx" value="1"/>
359 <param name="inputy" value="1"/>
360 </repeat> 525 </repeat>
361 </conditional> 526 </conditional>
527 <param name="grid_variable" value="TRUE"/>
362 <output name="plots" file="Plot_imzml.pdf" compare="sim_size"/> 528 <output name="plots" file="Plot_imzml.pdf" compare="sim_size"/>
363 </test> 529 </test>
364 <test> 530 <test>
365 <expand macro="infile_analyze75"/> 531 <expand macro="infile_analyze75"/>
366 <conditional name="pixel_conditional"> 532 <conditional name="pixel_conditional">
367 <param name="pixel_type" value="single_pixel"/> 533 <param name="pixel_type" value="tabular_pixel"/>
368 <repeat name="repeatpixel"> 534 <param name="pixel_file" value="spectra_1_pixel.tabular"/>
369 <param name="plusminusinDalton" value="0.25"/> 535 <param name="column_pixel_x" value="1"/>
370 <param name="inputx" value="5"/> 536 <param name="column_pixel_y" value="2"/>
371 <param name="inputy" value="2"/> 537 <param name="tabular_pixel_header" value="TRUE"/>
372 <repeat name="zoomedplot">
373 <param name="xlimmin" value="840"/>
374 <param name="xlimmax" value="850"/>
375 </repeat>
376 </repeat>
377 <repeat name="repeatpixel">
378 <param name="plusminusinDalton" value="0.25"/>
379 <param name="inputx" value="2"/>
380 <param name="inputy" value="2"/>
381 </repeat>
382 </conditional> 538 </conditional>
539 <param name="fullmz" value="TRUE"/>
540 <conditional name="mz_range">
541 <param name="mz_range_options" value="manual_mz"/>
542 <repeat name="zoomed_sample">
543 <param name="xlimmin" value="840"/>
544 <param name="xlimmax" value="850"/>
545 </repeat>
546 </conditional>
547 <param name="grid_variable" value="FALSE"/>
383 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size"/> 548 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size"/>
384 </test> 549 </test>
385 <test> 550 <test>
386 <expand macro="infile_analyze75"/> 551 <expand macro="infile_analyze75"/>
387 <conditional name="pixel_conditional"> 552 <conditional name="pixel_conditional">
388 <param name="pixel_type" value="sample_pixel"/> 553 <param name="pixel_type" value="tabular_pixel"/>
389 <conditional name="tabular_annotation"> 554 <param name="pixel_file" value="annotations.tabular"/>
390 555 <param name="column_pixel_x" value="1"/>
391 <param name="load_annotation" value="yes_annotation"/> 556 <param name="column_pixel_y" value="2"/>
392 <param name="annotation_file" value="annotations.tabular" ftype="tabular"/> 557 <param name="column_pixel_annotation" value="4"/>
393 <param name="column_x" value="1"/> 558 <param name="tabular_pixel_header" value="TRUE"/>
394 <param name="column_y" value="2"/> 559 </conditional>
395 <param name="column_names" value="4"/> 560 <param name="fullmz" value="FALSE"/>
396 <param name="tabular_header" value="TRUE"/> 561 <conditional name="mz_range">
397 562 <param name="mz_range_options" value="manual_mz"/>
398 563 <repeat name="zoomed_sample">
399 564 <param name="xlimmin" value="1250"/>
565 <param name="xlimmax" value="1270"/>
566 </repeat>
400 </conditional> 567 </conditional>
401 <repeat name="zoomed_sample"> 568 <param name="grid_variable" value="FALSE"/>
402 <param name="xlimmin" value="1250"/>
403 <param name="xlimmax" value="1270"/>
404 </repeat>
405 </conditional>
406 <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/> 569 <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>
407 </test> 570 </test>
408 <test> 571 <test>
409 <param name="infile" value="3_files_combined.RData" ftype="rdata"/> 572 <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
410 <conditional name="pixel_conditional"> 573 <conditional name="pixel_conditional">
411 <param name="pixel_type" value="sample_pixel"/> 574 <param name="pixel_type" value="all_pixel"/>
412 <repeat name="zoomed_sample">
413 <param name="xlimmin" value="350"/>
414 <param name="xlimmax" value="360"/>
415 </repeat>
416 </conditional> 575 </conditional>
576 <param name="fullmz" value="TRUE"/>
577 <conditional name="mz_range">
578 <param name="mz_range_options" value="manual_mz"/>
579 <repeat name="zoomed_sample">
580 <param name="xlimmin" value="350"/>
581 <param name="xlimmax" value="360"/>
582 </repeat>
583 </conditional>
584 <param name="grid_variable" value="FALSE"/>
417 <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/> 585 <output name="plots" file="Plot_rdata.pdf" compare="sim_size"/>
418 </test> 586 </test>
419 <test> 587 <test>
420 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> 588 <expand macro="processed_infile_imzml"/>
589 <conditional name="processed_cond">
590 <param name="processed_file" value="processed"/>
591 <param name="accuracy" value="50"/>
592 <param name="units" value="ppm"/>
593 </conditional>
421 <conditional name="pixel_conditional"> 594 <conditional name="pixel_conditional">
422 <param name="pixel_type" value="single_pixel"/> 595 <param name="pixel_type" value="all_pixel"/>
423 <repeat name="repeatpixel">
424 <param name="plusminusinDalton" value="0.1"/>
425 <param name="inputx" value="1"/>
426 <param name="inputy" value="1"/>
427 </repeat>
428 </conditional> 596 </conditional>
429 <output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size"/> 597 <param name="fullmz" value="FALSE"/>
598 <conditional name="mz_range">
599 <param name="mz_range_options" value="manual_mz"/>
600 <repeat name="zoomed_sample">
601 <param name="xlimmin" value="350"/>
602 <param name="xlimmax" value="350.5"/>
603 </repeat>
604 <repeat name="zoomed_sample">
605 <param name="xlimmin" value="600"/>
606 <param name="xlimmax" value="650"/>
607 </repeat>
608 </conditional>
609 <param name="grid_variable" value="TRUE"/>
610 <output name="plots" file="Plot_processed.pdf" compare="sim_size"/>
611 </test>
612 <test>
613 <param name="infile" value="" ftype="imzml">
614 <composite_data value="preprocessing_results1.imzml"/>
615 <composite_data value="preprocessing_results1.ibd"/>
616 </param>
617 <param name="centroids" value="TRUE"/>
618 <conditional name="pixel_conditional">
619 <param name="pixel_type" value="all_pixel"/>
620 </conditional>
621 <param name="fullmz" value="TRUE"/>
622 <conditional name="mz_range">
623 <param name="mz_range_options" value="manual_mz"/>
624 <repeat name="zoomed_sample">
625 <param name="xlimmin" value="328"/>
626 <param name="xlimmax" value="330"/>
627 </repeat>
628 <repeat name="zoomed_sample">
629 <param name="xlimmin" value="335"/>
630 <param name="xlimmax" value="340"/>
631 </repeat>
632 </conditional>
633 <param name="grid_variable" value="TRUE"/>
634 <output name="plots" file="Plot_picked.pdf" compare="sim_size"/>
430 </test> 635 </test>
431 </tests> 636 </tests>
432 <help><![CDATA[ 637 <help><![CDATA[
433 638
434 @CARDINAL_DESCRIPTION@ 639 @CARDINAL_DESCRIPTION@
436 ----- 641 -----
437 642
438 This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data. 643 This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass spectrometry imaging data.
439 644
440 @MSIDATA_INPUT_DESCRIPTION@ 645 @MSIDATA_INPUT_DESCRIPTION@
646
441 @SPECTRA_TABULAR_INPUT_DESCRIPTION@ 647 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
442 648
649 @MZ_TABULAR_INPUT_DESCRIPTION@
650
443 **Options** 651 **Options**
444 652
445 - "single pixel": Returns a full mass spectrum plot for one pixel, which is defined by its x- and y-coordinates 653 *Choosing spectra*
446 654
447 - Enter the x and y coordinates of your pixel of interest 655 - "All spectra": Plots average mass spectra (mean of all spectra)
448 - To have a visual control for the selected pixel, a heatmap of a m/z of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an m/z of interest together with a m/z range and for the lines the colour and type. 656
449 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot 657 - "Single spectra": Returns a full mass spectrum plot for each input spectrum, which is defined by its x- and y-coordinates
450 658
451 - "All pixels of a sample": Returns a full average mass spectrum plot with different colours for each pixel annotation group, without annotations the average of all pixels is plotted 659 - the annotation column is optional:
452 660 - without annotation column: plots a separate mass spectrum for every input spectrum
453 - Additionally zoom into mass spectra plots is possible by providing the minimum and maximum m/z value to define the limits of the plot 661 - with annotation column: plots average mass spectra for each annotation group in different colours
454 662
455 663
456 **Tip** 664 *Choosing m/z axis*
457 665
458 - Corresponding m/z intensity pairs for single spectra can be obtained with the filtering tool option "ranges for x and y" and afterwards using the imzml tabular exporter tool 666 - "Plot complete m/z range": Full m/z range is plotted
459 - Plots will only be drawn for pixels that exist in the MSI data, pixel that are outside the dataset will be "False" in the overview table on the last page of the pdf 667
668 - "zoomed in m/z range": Only a customized m/z range is plotted
669
670
671 - "Manual input": Provide the minimum and maximum m/z value to define the m/z axis of the plot
672
673 - "Tabular input": File with m/z values of interest. Needs manual choice of m/z values to subtract and add from the input m/z values to generate the m/z axis of the plot
460 674
461 675
462 **Output** 676 **Output**
463 677
464 - Pdf with the selected mass spectra plots and additional x-y grid plots 678 - Single Pdf with all mass spectra plots
465 679
466 680
467 ]]> 681 ]]>
468 </help> 682 </help>
469 <expand macro="citations"/> 683 <expand macro="citations"/>