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.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, xml.target, quiet = T) : downloaded length 46163 != reported length 200 2: In download.file(xml.url, xml.target, quiet = T) : downloaded length 35310 != reported length 200 3: In download.file(xml.url, xml.target, quiet = T) : downloaded length 43249 != reported length 200 4: In download.file(xml.url, xml.target, quiet = T) : downloaded length 43229 != reported length 200 5: In download.file(xml.url, xml.target, 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 locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  pathview_1.10.1 org.Hs.eg.db_3.2.3 RSQLite_1.0.0  DBI_0.3.1 AnnotationDbi_1.32.3 IRanges_2.4.7  S4Vectors_0.8.11 stringr_1.0.0 affyPLM_1.46.0  preprocessCore_1.32.0 gcrma_2.42.0 affy_1.48.0-1  Biobase_2.30.0 BiocGenerics_0.16.1 limma_3.26.8 loaded via a namespace (and not attached):  graph_1.48.0 KEGGgraph_1.28.0 XVector_0.10.0  magrittr_1.5 splines_3.2.2 zlibbioc_1.16.0  R6_2.1.2 httr_1.1.0 tools_3.2.2  grid_3.2.2 png_0.1-7 affyio_1.40.0  Rgraphviz_2.14.0 KEGGREST_1.10.1 stringi_1.0-1  org.Rn.eg.db_3.2.3 BiocInstaller_1.20.1 Biostrings_2.38.4  XML_3.98-1.3 >