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
line wrap: on
line diff
--- 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 ##########