Mercurial > repos > galaxyp > cardinal_spectra_plots
diff spectra_plots.xml @ 3:58c4aef16eb0 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
| author | galaxyp |
|---|---|
| date | Thu, 28 Feb 2019 09:27:53 -0500 |
| parents | 3642ed221eb2 |
| children | 9b6b86e771c2 |
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--- a/spectra_plots.xml Fri Feb 15 10:23:28 2019 -0500 +++ b/spectra_plots.xml Thu Feb 28 09:27:53 2019 -0500 @@ -56,7 +56,7 @@ #if str($processed_cond.processed_file) == "processed": ##processed file needs to be converted into matrix to be able to replace NAs iData(msidata) <- iData(msidata)[] - spectra(msidata)[][is.na(spectra(msidata)[])] = 0 + spectra(msidata)[is.na(spectra(msidata))] = 0 #else spectra(msidata)[is.na(spectra(msidata))] = 0 #end if @@ -101,7 +101,7 @@ ##################### III) plot full mass spectrum ################# - plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy)) + plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy), main="Mass spectrum of full m/z range") ##################### IV) plot zoom-in mass spectrum ############### @@ -199,9 +199,9 @@ key_legend = TRUE }else{key_legend = FALSE} - plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE) + 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") }else{ - plot(msidata, pixel=1:ncol(msidata), key=TRUE)} + plot(msidata, pixel=1:ncol(msidata), key=TRUE, main="Average mass spectrum of full m/z range")} ##################### II) Sample: plot zoom-in mass spectrum ##########