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Question: ID unmatched in pathview
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gravatar for joseph
8 weeks ago by
joseph40
joseph40 wrote:

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        

ADD COMMENTlink modified 5 weeks ago by Mataivic0 • written 8 weeks ago by joseph40
0
gravatar for Luo Weijun
5 weeks ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

more information is needed to find out your problem. In R, you can do:

head(datainv)

 

what’s the output from above line?

ADD COMMENTlink written 5 weeks ago by Luo Weijun1.4k
0
gravatar for Mataivic
5 weeks ago by
Mataivic0
Mataivic0 wrote:

I got the same error, and it came out of nowhere whitout any modification of my code. I have just asked a question here :

Error in pathview - came out of nowhere without any source code modification

ADD COMMENTlink written 5 weeks ago by Mataivic0
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