Argument map.symbol converting IDs even when its value is FALSE
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Entering edit mode
@arthurvinx-13988
Last seen 2.3 years ago

Hi, I'm trying to generate an image of the hsa00010 KEGG pathway.

When I run the following code, the ECs are not replaced by the ENTREZ. Is this correct? I thought map.symbol = FALSE would prevent the automatic conversion to symbol.

What should I do to get an image in which the ENTREZ are the node labels?

pathway <- "hsa00010"
IDs <- NULL
species <- gsub("^([[:alpha:]]*).*$", "\\1", pathway)
if(is.null(IDs)){
  IDs <- keggLink(species, pathway)
  IDs <- gsub("^[[:alpha:]]*:(.*)$", "\\1", IDs)
}
pathway <- gsub("^[[:alpha:]]*(.*)$", "\\1", pathway)
now <- format(Sys.time(), "%Y-%m-%d--%H-%M-%S")
img <- pathview::pathview(gene.data = IDs,
                          pathway.id = pathway,
                          out.suffix = now,
                          species = species,
                          high = list(gene = "darkseagreen1"),
                          kegg.native = TRUE,
                          same.layer = FALSE,
                          new.signature = FALSE,
                          plot.col.key = FALSE,
                          map.symbol = FALSE,
                          gene.annotpkg = NA,
                          map.null = FALSE)

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=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252    LC_MONETARY=Portuguese_Brazil.1252
[4] LC_NUMERIC=C                       LC_TIME=Portuguese_Brazil.1252    

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0           pillar_1.3.1         compiler_3.5.1       plyr_1.8.4           XVector_0.22.0      
 [6] tools_3.5.1          zlibbioc_1.28.0      digest_0.6.18        bit_1.1-14           viridisLite_0.3.0   
[11] jsonlite_1.6         tibble_2.0.1         RSQLite_2.1.1        memoise_1.1.0        gtable_0.2.0        
[16] rlang_0.3.1          pkgconfig_2.0.2      png_0.1-7            pathview_1.22.3      KEGGgraph_1.42.0    
[21] graph_1.60.0         igraph_1.2.4         rstudioapi_0.9.0     DBI_1.0.0            Rgraphviz_2.26.0    
[26] curl_3.3             yaml_2.2.0           parallel_3.5.1       dplyr_0.8.0.1        httr_1.4.0          
[31] htmlwidgets_1.3      Biostrings_2.50.2    S4Vectors_0.20.1     IRanges_2.16.0       tidyselect_0.2.5    
[36] stats4_3.5.1         bit64_0.9-7          grid_3.5.1           glue_1.3.0           Biobase_2.42.0      
[41] data.table_1.12.0    R6_2.4.0             plotly_4.8.0         AnnotationDbi_1.44.0 XML_3.98-1.17       
[46] RedeR_1.30.0         tidyr_0.8.2          purrr_0.3.0          ggplot2_3.1.0        blob_1.1.1          
[51] magrittr_1.5         htmltools_0.3.6      scales_1.0.0         BiocGenerics_0.28.0  assertthat_0.2.0    
[56] KEGGREST_1.22.0      colorspace_1.4-0     lazyeval_0.2.1       munsell_0.5.0        crayon_1.3.4
pathview • 430 views
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Entering edit mode

I see that you bumped this thread. Fala português? According to the manual entry, I would also expect Entrez IDs when map.symbol = FALSE, same.layer = FALSE, and kegg.native = TRUE, as in your example.

map.symbol: logical, whether map gene IDs to symbols for gene node labels or use the graphic name from the KGML file. This option is only effective for kegg.native=FALSE or same.layer=FALSE when kegg.native=TRUE. For same.layer=TRUE when kegg.native=TRUE, the native KEGG labels will be kept. Default map.symbol=TRUE.

Have you tried to use gene.annotpkg = "org.Hs.eg.db" ?

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