When I currently use pathview to present the KEGG pathway, the errors always are coming from multiplex pathways. It looks about unmatched gene ID. Here’s the codes and error warnings.
> pathview(gene.data = datainv,pathway.id="04668",species="hsa",out.suffix = "TNF Signaling Pathway",kegg.native = TRUE,same.layer = TRUE)
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, :
unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", :
replacement has 75 rows, data has 96
> pathview(gene.data = datainv,pathway.id="04010",species="hsa",out.suffix = "MAPK Signaling Pathway",kegg.native = TRUE,same.layer = TRUE)
Info: Downloading xml files for hsa04010, 1/1 pathways..
Info: Downloading png files for hsa04010, 1/1 pathways..
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, :
unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", :
replacement has 120 rows, data has 124
> pathview(gene.data = datainv,pathway.id="04350",species="hsa",out.suffix = "TGF-beta Signaling Pathway",kegg.native = TRUE,same.layer = TRUE)
Info: Downloading xml files for hsa04350, 1/1 pathways..
Info: Downloading png files for hsa04350, 1/1 pathways..
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, :
unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", :
replacement has 45 rows, data has 55
> pathview(gene.data = datainv,pathway.id="04370",species="hsa",out.suffix = "VEGF Signaling Pathway",kegg.native = TRUE,same.layer = TRUE)
Info: Downloading xml files for hsa04370, 1/1 pathways..
Info: Downloading png files for hsa04370, 1/1 pathways..
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, :
unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Info: Working in directory /Users/juehou/Documents/Microarray Data/SysVac VAC/Analysis
Info: Writing image file hsa04370.VEGF Signaling Pathway.multi.png
> pathview(gene.data = datainv,pathway.id="04630",species="hsa",out.suffix = "Jak-STAT Signaling Pathway",kegg.native = TRUE,same.layer = TRUE)
Info: Downloading xml files for hsa04630, 1/1 pathways..
Info: Downloading png files for hsa04630, 1/1 pathways..
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, :
unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", :
replacement has 31 rows, data has 34
> pathview(gene.data = datainv,pathway.id="04064",species="hsa",out.suffix = "NF-kappa B Signaling Pathway",kegg.native = TRUE,same.layer = TRUE)
Info: Downloading xml files for hsa04064, 1/1 pathways..
Info: Downloading png files for hsa04064, 1/1 pathways..
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, :
unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", :
replacement has 84 rows, data has 124
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] GeneAnswers_2.18.0 RColorBrewer_1.1-2 Heatplus_2.22.0 MASS_7.3-47 RCurl_1.95-4.8
[6] bitops_1.0-6 igraph_1.0.1 GOstats_2.42.0 Category_2.42.0 Matrix_1.2-9
[11] GSEABase_1.38.0 graph_1.54.0 annotate_1.54.0 XML_3.98-1.6 KEGG.db_3.2.3
[16] RSQLite_1.1-2 pathview_1.16.0 org.Hs.eg.db_3.4.1 AnnotationDbi_1.38.0 IRanges_2.10.0
[21] S4Vectors_0.14.0 Biobase_2.36.0 BiocGenerics_0.22.0 BiocInstaller_1.26.0 clusterProfiler_3.4.0
[26] DOSE_3.2.0 VennDiagram_1.6.17 futile.logger_1.4.3 ggplot2_2.2.1
loaded via a namespace (and not attached):
[1] KEGGgraph_1.34.0 Rcpp_0.12.10 lattice_0.20-35 tidyr_0.6.1
[5] GO.db_3.4.1 png_0.1-7 Biostrings_2.44.0 digest_0.6.12
[9] R6_2.2.0 plyr_1.8.4 futile.options_1.0.0 httr_1.2.1
[13] zlibbioc_1.22.0 lazyeval_0.2.0 data.table_1.10.4 Rgraphviz_2.20.0
[17] qvalue_2.8.0 labeling_0.3 splines_3.4.0 BiocParallel_1.10.0
[21] downloader_0.4 stringr_1.2.0 munsell_0.4.3 fgsea_1.2.1
[25] compiler_3.4.0 KEGGREST_1.16.0 tibble_1.3.0 gridExtra_2.2.1
[29] AnnotationForge_1.18.0 RBGL_1.52.0 xtable_1.8-2 gtable_0.2.0
[33] DBI_0.6-1 magrittr_1.5 scales_0.4.1 stringi_1.1.5
[37] GOSemSim_2.2.0 genefilter_1.58.0 XVector_0.16.0 reshape2_1.4.2
[41] DO.db_2.9 rvcheck_0.0.8 fastmatch_1.1-0 lambda.r_1.1.9
[45] tools_3.4.0 survival_2.41-3 colorspace_1.3-2 memoise_1.1.0
>
