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I am using pathview to produce a native KEGG plot in PNG from results of gseKEGG analysis.
I have succesfully produced and downloaded PNGs of other pathways using the same command and dataset but get this error when running the specific pathway mmu04938
# i use the code below, where kegg_gene_list is my list of genes with entrez IDs and corresponding fold changes, and kegg_organism is org.Mm.eg.db
parathryoid <- pathview(gene.data = kegg_gene_list, pathway.id="mmu04928", species = kegg_organism)
# i get this error
Specification mandates value for attribute valu
attributes construct error
Couldn't find end of Start Tag subtype line 673
Premature end of data in tag relation line 672
Premature end of data in tag pathway line 4
Warning: Parsing ./mmu04928.xml file failed, please check the file!
sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pathview_1.36.0
loaded via a namespace (and not attached):
[1] fgsea_1.22.0 ggnewscale_0.4.7 colorspace_2.0-3 ggtree_3.4.0
[5] ellipsis_0.3.2 ggridges_0.5.3 qvalue_2.28.0 XVector_0.36.0
[9] aplot_0.1.6 rstudioapi_0.13 farver_2.1.0 graphlayouts_0.8.0
[13] ggrepel_0.9.1 bit64_4.0.5 AnnotationDbi_1.58.0 fansi_1.0.3
[17] scatterpie_0.1.7 codetools_0.2-18 splines_4.2.0 cachem_1.0.6
[21] GOSemSim_2.22.0 knitr_1.39 polyclip_1.10-0 jsonlite_1.8.0
[25] GO.db_3.15.0 png_0.1-7 graph_1.74.0 ggforce_0.3.3
[29] compiler_4.2.0 httr_1.4.3 assertthat_0.2.1 Matrix_1.4-1
[33] fastmap_1.1.0 lazyeval_0.2.2 cli_3.3.0 org.Mm.eg.db_3.15.0
[37] tweenr_1.0.2 tools_4.2.0 igraph_1.3.1 gtable_0.3.0
[41] glue_1.6.2 GenomeInfoDbData_1.2.8 reshape2_1.4.4 DO.db_2.9
[45] dplyr_1.0.9 fastmatch_1.1-3 Rcpp_1.0.8.3 enrichplot_1.16.1
[49] Biobase_2.56.0 vctrs_0.4.1 Biostrings_2.64.0 ape_5.6-2
[53] nlme_3.1-157 ggraph_2.0.5 xfun_0.31 stringr_1.4.0
[57] lifecycle_1.0.1 clusterProfiler_4.4.2 XML_3.99-0.9 DOSE_3.22.0
[61] org.Hs.eg.db_3.15.0 zlibbioc_1.42.0 MASS_7.3-57 scales_1.2.0
[65] tidygraph_1.2.1 parallel_4.2.0 KEGGgraph_1.56.0 RColorBrewer_1.1-3
[69] memoise_2.0.1 gridExtra_2.3 ggplot2_3.3.6 ggfun_0.0.6
[73] downloader_0.4 yulab.utils_0.0.4 stringi_1.7.6 RSQLite_2.2.14
[77] S4Vectors_0.34.0 tidytree_0.3.9 BiocGenerics_0.42.0 BiocParallel_1.30.3
[81] GenomeInfoDb_1.32.2 rlang_1.0.2 pkgconfig_2.0.3 bitops_1.0-7
[85] lattice_0.20-45 purrr_0.3.4 treeio_1.20.0 patchwork_1.1.1
[89] cowplot_1.1.1 shadowtext_0.1.2 bit_4.0.4 tidyselect_1.1.2
[93] plyr_1.8.7 magrittr_2.0.3 R6_2.5.1 IRanges_2.30.0
[97] generics_0.1.2 DBI_1.1.2 pillar_1.7.0 KEGGREST_1.36.0
[101] RCurl_1.98-1.6 tibble_3.1.7 crayon_1.5.1 utf8_1.2.2
[105] viridis_0.6.2 grid_4.2.0 data.table_1.14.2 Rgraphviz_2.40.0
[109] blob_1.2.3 digest_0.6.29 tidyr_1.2.0 gridGraphics_0.5-1
[113] stats4_4.2.0 munsell_0.5.0 viridisLite_0.4.0 ggplotify_0.1.0
Can anyone help me out with this? I have made over 10 other native KEGG plots and am stuck on the last one.
All my packages are up to date and I am using the latest version of R.
Thanks
