Argument map.symbol converting IDs even when its value is FALSE
Entering edit mode
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"
species <- gsub("^([[:alpha:]]*).*$", "\\1", pathway)
  IDs <- keggLink(species, pathway)
  IDs <- gsub("^[[:alpha:]]*:(.*)$", "\\1", IDs)
pathway <- gsub("^[[:alpha:]]*(.*)$", "\\1", pathway)
now <- format(Sys.time(), "%Y-%m-%d--%H-%M-%S")
img <- pathview::pathview( = IDs,
                 = 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)


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

[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
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 = "" ?


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