Mercurial > repos > galaxyp > cardinal_filtering

comparison filtering.xml @ 10:a4475567dd22 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca89f8e007c6b17f7c30066729e05b8686ab975a"
author galaxyp
date Sun, 27 Sep 2020 10:54:29 +0000
parents e92efed83208
children 105056844497
comparison
equal deleted inserted replaced
9:e92efed83208 10:a4475567dd22
384 theme(legend.position="bottom",legend.direction="vertical")+ 384 theme(legend.position="bottom",legend.direction="vertical")+
385 labs(title="Overview of filtered m/z", x="m/z", y = "count") + 385 labs(title="Overview of filtered m/z", x="m/z", y = "count") +
386 guides(fill=guide_legend(ncol=5,byrow=TRUE)) 386 guides(fill=guide_legend(ncol=5,byrow=TRUE))
387 print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D"))) 387 print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
388 388
389 389 dev.off()
390
391 dev.off()
392 390
393 ## save msidata as imzML file, will only work if there is at least 1 m/z left 391 ## save msidata as imzML file, will only work if there is at least 1 m/z left
394 392
395 if (maxfeatures2 > 0){ 393 if (maxfeatures2 > 0){
396 ## make sure that coordinates are integers 394 ## make sure that coordinates are integers
397 coord(msidata)\$y = as.integer(coord(msidata)\$y) 395 coord(msidata)\$y = as.integer(coord(msidata)\$y)
398 coord(msidata)\$x = as.integer(coord(msidata)\$x) 396 coord(msidata)\$x = as.integer(coord(msidata)\$x)
397 msidata = as(msidata, "MSContinuousImagingExperiment")
399 writeImzML(msidata, "out")} 398 writeImzML(msidata, "out")}
400 399
401 400
402 }else{ 401 }else{
403 print("Inputfile or filtered file has no intensities > 0") 402 print("Inputfile or filtered file has no intensities > 0")