datapplab / pathview

pathway based data integration and visualization
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Cannot output any pseudo colours #21

Open LuoJulia opened 2 years ago

LuoJulia commented 2 years ago

Hello - my issue is the title: I'm unable to output any pseudocolour range in my pathview plots, they are all coloured the same green shade. I'm not sure if I don't have my pathview function set up correctly -- would appreciate any help! Thank you!

Here is the example code I am running & the output I get:

mypathway<-"vvi03060"
genes<-c("100241050","100243802","100244217","100244265","100247624","100247887","100248517","
100248990","100250268","100250385","100250458","100251379","100252350","100252527","100252725","
100252902","100253826","100254350","100254429","100254996","100255515","100256046","100256113","
100256412","100256941","100257568","100257730","100258179","100258854","100259285","100259443","
100260422","100260431","100261219","100262919","100263033","100264739","100265371","100266802","
100267343","100267692","100852861","100853033","100854110","100854416","100854647","100855182","
104879783","109122671")
logFC<-rnorm(length(genes),-0.5,1)
names(logFC)<-genes
pathview(gene.data=logFC,species="vvi",kegg.dir = paste0(pathPlots), pathway=mypathway)

Result is the same if I add limit = list(gene=c(-2,2), cpd=1) or limit = list(gene=1, cpd=1) as an argument.

vvi03060

Session Info: R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages: [1] pathview_1.36.1 org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0 IRanges_2.30.1 S4Vectors_0.34.0 Biobase_2.56.0
[7] BiocGenerics_0.42.0 RColorBrewer_1.1-3 ggplot2_3.3.6 dplyr_1.0.10

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 XVector_0.36.0 GenomeInfoDb_1.32.4 pillar_1.8.1 compiler_4.2.1
[6] zlibbioc_1.42.0 bitops_1.0-7 tools_4.2.1 bit_4.0.4 RSQLite_2.2.18
[11] memoise_2.0.1 lifecycle_1.0.2 tibble_3.1.8 gtable_0.3.1 png_0.1-7
[16] pkgconfig_2.0.3 rlang_1.0.6 graph_1.74.0 KEGGgraph_1.56.0 cli_3.4.1
[21] DBI_1.1.3 Rgraphviz_2.40.0 fastmap_1.1.0 GenomeInfoDbData_1.2.8 httr_1.4.4
[26] withr_2.5.0 Biostrings_2.64.1 generics_0.1.3 vctrs_0.4.2 bit64_4.0.5
[31] grid_4.2.1 tidyselect_1.1.2 glue_1.6.2 R6_2.5.1 fansi_1.0.3
[36] XML_3.99-0.11 purrr_0.3.4 blob_1.2.3 magrittr_2.0.3 scales_1.2.1
[41] KEGGREST_1.36.3 colorspace_2.0-3 utf8_1.2.2 RCurl_1.98-1.9 munsell_0.5.0
[46] cachem_1.0.6 crayon_1.5.2