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