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Question: ReactomePA viewPathway DE node and legend colour
1
gravatar for Kajus Baidžajevas
10 months ago by
University of Sheffield
Kajus Baidžajevas10 wrote:

Hello,

I am visualising RNA-seq data in reactome pathways using ReactomePA. I have a range of gene expression fold changes (FCs) among multiple conditions.

> cond1FC
 335  338 6288  948  949 
  -5   -3    0    1    4 
> cond2FC
  335   338  6288   948   949 
-0.30 -0.10 -0.05  0.05  0.06 

viewPathway in ReactomePA (and by extension netplot in DOSE) return images with nodes and FC scales coloured adjusted to the range of FC values in each condition separately.

> viewPathway("Scavenging by Class B Receptors", organism = "human", readable = TRUE, foldChange = cond1FC, vertex.label.font = 3, vertex.label.cex = 0.7, col.bin = 10, legend.x = 1, legend.y = 1, fixed = TRUE, vertex.size = 10)
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

http://imgur.com/w77zQO4

> viewPathway("Scavenging by Class B Receptors", organism = "human", readable = TRUE, foldChange = cond2FC, vertex.label.font = 3, vertex.label.cex = 0.7, col.bin = 10, legend.x = 1, legend.y = 1, fixed = TRUE, vertex.size = 10)
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

http://imgur.com/U3lNIxX

Is there a way that the colour range could be customised/standardised (in the case above from -5 to 5 fold change) so that each FC value would have the same shade in each condition despite widely different FC value ranges in each condition?

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
 [1] BiocInstaller_1.24.0   graphite_1.20.1        ReactomePA_1.18.1     
 [4] DOSE_3.0.9             org.Hs.eg.db_3.4.0     goseq_1.26.0          
 [7] geneLenDataBase_1.10.0 BiasedUrn_1.07         RpsiXML_2.16.0        
[10] hypergraph_1.46.0      RBGL_1.50.0            annotate_1.52.1       
[13] XML_3.98-1.5           AnnotationDbi_1.36.1   IRanges_2.8.1         
[16] S4Vectors_0.12.1       Biobase_2.34.0         graph_1.52.0          
[19] BiocGenerics_0.20.0   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8                lattice_0.20-33           
 [3] GO.db_3.4.0                Rsamtools_1.26.1          
 [5] Biostrings_2.42.1          assertthat_0.1            
 [7] digest_0.6.11              GenomeInfoDb_1.10.2       
 [9] plyr_1.8.4                 RSQLite_1.1-2             
[11] ggplot2_2.2.1              zlibbioc_1.20.0           
[13] GenomicFeatures_1.26.2     lazyeval_0.2.0            
[15] data.table_1.10.0          Matrix_1.2-6              
[17] qvalue_2.6.0               devtools_1.12.0           
[19] splines_3.3.1              BiocParallel_1.8.1        
[21] stringr_1.1.0              igraph_1.0.1              
[23] RCurl_1.95-4.8             biomaRt_2.30.0            
[25] munsell_0.4.3              fgsea_1.0.2               
[27] rtracklayer_1.34.1         mgcv_1.8-12               
[29] SummarizedExperiment_1.4.0 tibble_1.2                
[31] gridExtra_2.2.1            withr_1.0.2               
[33] GenomicAlignments_1.10.0   bitops_1.0-6              
[35] rappdirs_0.3.1             grid_3.3.1                
[37] nlme_3.1-128               xtable_1.8-2              
[39] gtable_0.2.0               DBI_0.5-1                 
[41] magrittr_1.5               scales_0.4.1              
[43] stringi_1.1.2              GOSemSim_2.0.3            
[45] XVector_0.14.0             reshape2_1.4.2            
[47] DO.db_2.9                  rvcheck_0.0.5             
[49] fastmatch_1.0-4            tools_3.3.1               
[51] colorspace_1.3-2           reactome.db_1.58.0        
[53] GenomicRanges_1.26.2       memoise_1.0.0       
> rvcheck::check_bioc("ReactomePA")
package is up-to-date release version
$package
[1] "ReactomePA"

$installed_version
[1] "1.18.1"

$latest_version
[1] "1.18.1"

$up_to_date
[1] TRUE

> rvcheck::check_bioc("reactome.db")
package is up-to-date release version
$package
[1] "reactome.db"

$installed_version
[1] "1.58.0"

$latest_version
[1] "1.58.0"

$up_to_date
[1] TRUE

> rvcheck::check_bioc("DOSE")
package is up-to-date release version
$package
[1] "DOSE"

$installed_version
[1] "3.0.9"

$latest_version
[1] "3.0.9"

$up_to_date
[1] TRUE
> rvcheck::check_bioc("graphite")
package is up-to-date release version
$package
[1] "graphite"

$installed_version
[1] "1.20.1"

$latest_version
[1] "1.20.1"

$up_to_date
[1] TRUE

Thank you,

Kajus

ADD COMMENTlink written 10 months ago by Kajus Baidžajevas10

Currently, it is not supported.

 

ADD REPLYlink written 10 months ago by Guangchuang Yu800
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