Error in array(col.rgb[, i], dim(node.rgb)[3:1])

[Asa12138]

An error will be reported when drawing certain pathways, such as map01230, because there is no rectangle of gene, but the hsa01230.png image is still generated under the folder.

data(gse16873.d)
data(demo.paths)
> pv.out <- pathview::pathview(gene.data = gse16873.d[, 1], pathway.id = "01230")
Info: Downloading xml files for hsa01230, 1/1 pathways..
Info: Downloading png files for hsa01230, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /Users/asa/Documents/R/MASS_cohort/analysis
Info: Writing image file hsa01230.pathview.png
Info: some node width is different from others, and hence adjusted!
Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : 
  negative length vectors are not allowed

[ashfricker]

I have the same issues with some maps.
The problem only arises when I set both kegg.native=TRUE and same.layer=TRUE.
However, if kegg.native=FALSE and same.layer=TRUE, the graph renders chaotically with colors.
If kegg.native=TRUE and same.layer=FALSE, the graph renders as the base KEGG map (no color overlay).

head(Merge.path)

Output:
logFC.1 logFC.2
K00008 1.0303669 1.07015474
K00010 0.0000000 0.71213278
K00020 0.3793045 0.00000000
K00025 0.0000000 0.92373297
K00027 0.0000000 0.12629341
K00030 0.0000000 0.02248162
^ Data is set as a dataframe with two (bacterial) species' logFC values.

pv.out <- pathview(gene.data = Merge.path, 
         pathway.id = "01200", 
         species="ko", 
         low = "blue", 
         mid = "grey", 
         high = "red", 
         limit = list(gene=max(Merge.path)),
         kegg.native = TRUE,
         same.layer = TRUE,
         both.dirs = TRUE)

Error in array(col.rgb[, i], dim(node.rgb)[3:1]) :
negative length vectors are not allowed