Hi,

I met an error when using the TOMplot function of WGCNA. The plot was not labeled with any color and the following warning messages were returned:

Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
  "colors" is not a graphical parameter
2: In doTryCatch(return(expr), name, parentenv, handler) :
  "colors" is not a graphical parameter
3: In doTryCatch(return(expr), name, parentenv, handler) :
  "colors" is not a graphical parameter
4: In doTryCatch(return(expr), name, parentenv, handler) :
  reached elapsed time limit
5: In doTryCatch(return(expr), name, parentenv, handler) :
  "colors" is not a graphical parameter
6: In doTryCatch(return(expr), name, parentenv, handler) :
  "colors" is not a graphical parameter
7: In doTryCatch(return(expr), name, parentenv, handler) :
  "colors" is not a graphical parameter

I ran the command lines included in the tutorial of WGCNA:

A = adjacency(datExprFemale, power = 6) 

dissTOM =TOMdist(A) 

diag(dissTOM) = NA 
TOMplot(dissim=dissTOM^7,dendro=geneTree,colors=moduleColorsFemale, main = "Network heatmap 
plot, all genes") 

> sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Do you know what caused the error? Thank you!

The relevant argument in TOMplot is Colors, not colors. Try supplying Colors, not colors.

Peter