Mercurial > repos > galaxyp > cardinal_filtering
comparison filtering.xml @ 10:a4475567dd22 draft
"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 |
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| 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") |