KEGG pictures were not colored

[powerhorse1986]

Describe the bug The pictures downloaded from KEGG were not colored by red/blue.

To Reproduce Steps to reproduce the behavior:

1. Executing run_pathfindR(input_df, max_to_plot = 25)

Expected behavior The pictures should be colored by the red color or the blue color based on the status of corresponding genes.

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Ubuntu
• Version: 20.04

R Session Information: Please provide the R session information (by running sessionInfo()) R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] magrittr_2.0.3 pathfindR_1.6.3.9006 pathfindR.data_1.1.2 org.Hs.eg.db_3.15.0 AnnotationDbi_1.58.0 rtracklayer_1.56.1
[7] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[13] tibble_3.1.7 ggplot2_3.3.6 tidyverse_1.3.1 fdrtool_1.2.17 RColorBrewer_1.1-3 gplots_3.1.3
[19] gprofiler2_0.2.1 gProfileR_0.7.0 biomaRt_2.52.0 DESeq2_1.36.0 SummarizedExperiment_1.26.1 Biobase_2.56.0
[25] MatrixGenerics_1.8.1 matrixStats_0.62.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0
[31] BiocGenerics_0.42.0 RSQLite_2.2.14

loaded via a namespace (and not attached): [1] utf8_1.2.2 tidyselect_1.1.2 htmlwidgets_1.5.4 grid_4.2.1 BiocParallel_1.30.3 devtools_2.4.3 munsell_0.5.0
[8] codetools_0.2-18 withr_2.5.0 colorspace_2.0-3 filelock_1.0.2 highr_0.9 knitr_1.39 rstudioapi_0.13
[15] labeling_0.4.2 KEGGgraph_1.56.0 GenomeInfoDbData_1.2.8 mixsqp_0.3-43 polyclip_1.10-0 bit64_4.0.5 farver_2.1.0
[22] rprojroot_2.0.3 vctrs_0.4.1 generics_0.1.2 xfun_0.31 BiocFileCache_2.4.0 R6_2.5.1 doParallel_1.0.17
[29] graphlayouts_0.8.0 invgamma_1.1 locfit_1.5-9.5 bitops_1.0-7 cachem_1.0.6 DelayedArray_0.22.0 assertthat_0.2.1
[36] BiocIO_1.6.0 scales_1.2.0 ggraph_2.0.5 gtable_0.3.0 processx_3.6.1 tidygraph_1.2.1 rlang_1.0.3
[43] genefilter_1.78.0 splines_4.2.1 lazyeval_0.2.2 broom_0.8.0 yaml_2.3.5 modelr_0.1.8 backports_1.4.1
[50] tools_4.2.1 usethis_2.1.6 ellipsis_0.3.2 jquerylib_0.1.4 sessioninfo_1.2.2 Rcpp_1.0.8.3 progress_1.2.2
[57] zlibbioc_1.42.0 RCurl_1.98-1.7 ps_1.7.1 prettyunits_1.1.1 viridis_0.6.2 ashr_2.2-54 haven_2.5.0
[64] ggrepel_0.9.1 fs_1.5.2 data.table_1.14.2 magick_2.7.3 reprex_2.0.1 truncnorm_1.0-8 SQUAREM_2021.1
[71] pkgload_1.3.0 hms_1.1.1 evaluate_0.15 xtable_1.8-4 XML_3.99-0.10 readxl_1.4.0 gridExtra_2.3
[78] compiler_4.2.1 KernSmooth_2.23-20 crayon_1.5.1 htmltools_0.5.2 tzdb_0.3.0 geneplotter_1.74.0 lubridate_1.8.0
[85] DBI_1.1.3 tweenr_1.0.2 dbplyr_2.2.1 MASS_7.3-57 rappdirs_0.3.3 Matrix_1.4-1 cli_3.3.0
[92] parallel_4.2.1 igraph_1.3.2 pkgconfig_2.0.3 GenomicAlignments_1.32.0 plotly_4.10.0 xml2_1.3.3 foreach_1.5.2
[99] annotate_1.74.0 bslib_0.3.1 XVector_0.36.0 rvest_1.0.2 callr_3.7.0 digest_0.6.29 graph_1.74.0
[106] Biostrings_2.64.0 rmarkdown_2.14 cellranger_1.1.0 restfulr_0.0.15 curl_4.3.2 Rsamtools_2.12.0 gtools_3.9.2.2
[113] rjson_0.2.21 lifecycle_1.0.1 jsonlite_1.8.0 viridisLite_0.4.0 fansi_1.0.3 pillar_1.7.0 lattice_0.20-45
[120] KEGGREST_1.36.2 fastmap_1.1.0 httr_1.4.3 pkgbuild_1.3.1 survival_3.3-1 glue_1.6.2 remotes_2.4.2
[127] png_0.1-7 iterators_1.0.14 bit_4.0.4 Rgraphviz_2.40.0 ggforce_0.3.3 stringi_1.7.6 sass_0.4.1
[134] blob_1.2.3 caTools_1.18.2 memoise_2.0.1 irlba_2.3.5

Additional context I raised an issue yesterday which reported the problem with downloading the png pics from KEGG. And it's been solved by updating the package "KEGGREST". However, I found that the downloaded pics were not colored as before. I used the same dataset.

[egeulgen]

this is another issue with KEGGREST, which I raised with them will update you and #125 as soon as I hear from them

[egeulgen]

KEGGREST recently fixed this issue. Please update via:

devtools::install_github("Bioconductor/KEGGREST")