Question: Pathview: visualization of data
gravatar for Guido Hooiveld
3.1 years ago by
Guido Hooiveld2.4k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.4k wrote:

Dear Weijun,

I am using your very nice package Pathview to visualize my expression data, and I am fine-tuning the graphical output towards my needs. I therefore have 3 questions, and would appreciate if you could comment on these:

- I would like to visualize (overlay) the expression data of 6 conditions (comparisons) on the nodes of a pathway. This goes fine, but because the relative small size of the "bars" (representing each condition) when overlaid on the nodes it is sometimes difficult to see whether for example it is the 3rd or rather the 4th condition that is (more) regulated compared to the other conditions. I therefore would like to ask whether it somehow would be possible to separate each "bar" by e.g. a thin gray or black line (thus add a border to each "bar").

- what exactly is the difference between node.sum="max" and node.sum="max.abs"? This is not clear from the help pages.

- what do the color scale bars represent? (-1 = green, 0 = gray, +1 = red). Am i correct that it reflects the row-standardized expression values?


Lastly, are this warnings indicating something serious? (Obtained when overlying data on 5 pathways).

Warning messages:
1: In download.file(xml.url,, quiet = T) :
  downloaded length 46163 != reported length 200
2: In download.file(xml.url,, quiet = T) :
  downloaded length 35310 != reported length 200
3: In download.file(xml.url,, quiet = T) :
  downloaded length 43249 != reported length 200
4: In download.file(xml.url,, quiet = T) :
  downloaded length 43229 != reported length 200
5: In download.file(xml.url,, quiet = T) :
  downloaded length 44976 != reported length 200





> sessionInfo()
R version 3.2.2 Patched (2015-11-03 r69595)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] pathview_1.10.1    RSQLite_1.0.0        
 [4] DBI_0.3.1             AnnotationDbi_1.32.3  IRanges_2.4.7        
 [7] S4Vectors_0.8.11      stringr_1.0.0         affyPLM_1.46.0       
[10] preprocessCore_1.32.0 gcrma_2.42.0          affy_1.48.0-1        
[13] Biobase_2.30.0        BiocGenerics_0.16.1   limma_3.26.8         

loaded via a namespace (and not attached):
 [1] graph_1.48.0         KEGGgraph_1.28.0     XVector_0.10.0      
 [4] magrittr_1.5         splines_3.2.2        zlibbioc_1.16.0     
 [7] R6_2.1.2             httr_1.1.0           tools_3.2.2         
[10] grid_3.2.2           png_0.1-7            affyio_1.40.0       
[13] Rgraphviz_2.14.0     KEGGREST_1.10.1      stringi_1.0-1       
[16]   BiocInstaller_1.20.1 Biostrings_2.38.4   
[19] XML_3.98-1.3        
ADD COMMENTlink modified 3.0 years ago by Luo Weijun1.4k • written 3.1 years ago by Guido Hooiveld2.4k
Answer: Pathview: visualization of data
gravatar for Luo Weijun
3.0 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Guido, We oringally separate each sample (color block) by a black line. But we found that line interfere with the actual color blocks (i.e. with similar width) when the number of samples become big. It becomes a rather messy view that way. Some users complained on the black lines even when there are only 2-3 samples. Anyway, pathview does not do that border line for a good reason. node.sum="max" and node.sum="max.abs" means either to use the gene with maximal value or the maximal absolute value as the summary/representative of a node when it includes multiple genes. In pathview, the color-coded values are original not standardized. The color key gives the range, values beyond that range are coverted to the closest extreme, i.e. values>1 converted to 1, and values< -1 converted to -1. Please check arguments limit, low, mid, high in pathview documentation: ?pathview
ADD COMMENTlink written 3.0 years ago by Luo Weijun1.4k
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