Question: TOMplot error: "color" is not a graphical parameter (WGCNA)
0
gravatar for giuseppe0525
8 months ago by
giuseppe05250 wrote:

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!

ADD COMMENTlink modified 8 months ago by Peter Langfelder2.1k • written 8 months ago by giuseppe05250
Answer: TOMplot error: "color" is not a graphical parameter (WGCNA)
0
gravatar for Peter Langfelder
8 months ago by
United States
Peter Langfelder2.1k wrote:

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

Peter

ADD COMMENTlink written 8 months ago by Peter Langfelder2.1k

Thank you very much! I didn't notice it.

ADD REPLYlink written 8 months ago by giuseppe05250
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