--- a/filtering.xml	Wed May 13 17:54:30 2020 +0000
+++ b/filtering.xml	Tue Nov 03 22:26:34 2020 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2.3">r-gridextra</requirement>
-        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
+        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
     </expand>
     <expand macro="print_version"/>
     <command detect_errors="exit_code">
@@ -365,7 +365,7 @@
            theme(plot.title = element_text(hjust = 0.5))+
            theme(legend.position="bottom",legend.direction="vertical")+
            guides(fill=guide_legend(ncol=5,byrow=TRUE))
-    print(pixel_image)
+    print(pixel_image + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
 
 
     ### visual mz feature control
@@ -384,10 +384,9 @@
         theme(legend.position="bottom",legend.direction="vertical")+
         labs(title="Overview of filtered m/z", x="m/z", y = "count") +
         guides(fill=guide_legend(ncol=5,byrow=TRUE))
-      print(histogram_mz)
+      print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D")))
 
-
-        dev.off()
+    dev.off()
 
     ## save msidata as imzML file, will only work if there is at least 1 m/z left
 
@@ -395,6 +394,7 @@
             ## make sure that coordinates are integers
             coord(msidata)\$y = as.integer(coord(msidata)\$y)
             coord(msidata)\$x = as.integer(coord(msidata)\$x)
+            msidata = as(msidata, "MSContinuousImagingExperiment")
         writeImzML(msidata, "out")}
 
 
@@ -525,7 +525,7 @@
             <expand macro="processed_infile_imzml"/>
             <conditional name="processed_cond">
                 <param name="processed_file" value="processed"/>
-                <param name="accuracy" value="100"/>
+                <param name="accuracy" value="200"/>
                 <param name="units" value="ppm"/>
             </conditional>
             <param name="pixel_filtering" value="two_columns"/>