Pathview won't render some KEGG pathways
1
0
Entering edit mode
Duncan • 0
@0e15754d
Last seen 15 months ago
South Africa

Problem

I'm running a script to generate pathway visualisations for a list of interesting pathways. The script uses pathview. On most of my pathways this works, but with some of them, I get an error.

Error message

Error in cut.default(node.summary, data.cuts, include.lowest = TRUE, right = F) : 
  'breaks' are not unique

Reproducible example

# command
pv_out = pathview(
  gene.data = geneData,
  pathway.id = "05120",
  species = "hsa",
  same.layer = TRUE,
  out.suffix = "Epithelial_cell_signaling_in_Helicobacter_pylori_infection",
  limit = list(
    gene = c(-3, 8),
    cpd = c(1, 1)
  )
)

# where "geneData" is the following:

> geneData
         lfc_mean
51606   2.2439377
537     1.9637509
4790    0.4912091
10312   2.2125236
1839    5.5535664
533     1.1882902
529     0.9639135
526     1.6909496
245972  4.5743062
6868    2.5705107
528     1.4247033
5603    3.4382452
50848   1.8549717
9114    1.3987230
3576    7.4946791
5970    1.1179397
3725    3.8582940
6300   -2.7698144

# resulting error

Error in cut.default(node.summary, data.cuts, include.lowest = TRUE, right = F) : 
  'breaks' are not unique

Thanks in advance for your help.

Session info

# sessionInfo()

R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

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

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

other attached packages:
 [1] pathview_1.30.1        ggnewscale_0.4.5       forcats_0.5.1         
 [4] stringr_1.4.0          dplyr_1.0.3            purrr_0.3.4           
 [7] readr_1.4.0            tidyr_1.1.2            tibble_3.0.6          
[10] ggplot2_3.3.3          tidyverse_1.3.0        biomaRt_2.46.3        
[13] org.Hs.eg.db_3.12.0    AnnotationDbi_1.52.0   IRanges_2.24.1        
[16] S4Vectors_0.28.1       Biobase_2.50.0         BiocGenerics_0.36.0   
[19] clusterProfiler_3.18.1

loaded via a namespace (and not attached):
  [1] readxl_1.3.1                shadowtext_0.0.7            backports_1.2.1            
  [4] fastmatch_1.1-0             BiocFileCache_1.14.0        plyr_1.8.6                 
  [7] igraph_1.2.6                splines_4.0.5               BiocParallel_1.24.1        
 [10] GenomeInfoDb_1.26.2         digest_0.6.27               GOSemSim_2.16.1            
 [13] viridis_0.5.1               GO.db_3.12.1                magrittr_2.0.1             
 [16] memoise_2.0.0               Biostrings_2.58.0           annotate_1.68.0            
 [19] graphlayouts_0.7.1          modelr_0.1.8                matrixStats_0.58.0         
 [22] askpass_1.1                 enrichplot_1.10.2           prettyunits_1.1.1          
 [25] colorspace_2.0-0            blob_1.2.1                  rvest_0.3.6                
 [28] rappdirs_0.3.3              ggrepel_0.9.1               haven_2.3.1                
 [31] crayon_1.4.0                RCurl_1.98-1.2              jsonlite_1.7.2             
 [34] graph_1.68.0                scatterpie_0.1.5            genefilter_1.72.1          
 [37] survival_3.2-7              glue_1.4.2                  polyclip_1.10-0            
 [40] gtable_0.3.0                zlibbioc_1.36.0             XVector_0.30.0             
 [43] DelayedArray_0.16.1         Rgraphviz_2.34.0            scales_1.1.1               
 [46] DOSE_3.16.0                 DBI_1.1.1                   Rcpp_1.0.6                 
 [49] viridisLite_0.3.0           xtable_1.8-4                progress_1.2.2             
 [52] bit_4.0.4                   httr_1.4.2                  fgsea_1.16.0               
 [55] RColorBrewer_1.1-2          ellipsis_0.3.1              pkgconfig_2.0.3            
 [58] XML_3.99-0.5                farver_2.0.3                dbplyr_2.0.0               
 [61] locfit_1.5-9.4              tidyselect_1.1.0            labeling_0.4.2             
 [64] rlang_0.4.10                reshape2_1.4.4              munsell_0.5.0              
 [67] cellranger_1.1.0            tools_4.0.5                 cachem_1.0.1               
 [70] downloader_0.4              cli_2.3.0                   generics_0.1.0             
 [73] RSQLite_2.2.3               broom_0.7.4                 fastmap_1.1.0              
 [76] bit64_4.0.5                 fs_1.5.0                    tidygraph_1.2.0            
 [79] KEGGREST_1.30.1             ggraph_2.0.5                KEGGgraph_1.50.0           
 [82] DO.db_2.9                   xml2_1.3.2                  compiler_4.0.5             
 [85] rstudioapi_0.13             curl_4.3                    png_0.1-7                  
 [88] reprex_1.0.0                tweenr_1.0.1                geneplotter_1.68.0         
 [91] stringi_1.5.3               lattice_0.20-41             Matrix_1.3-2               
 [94] vctrs_0.3.6                 pillar_1.4.7                lifecycle_0.2.0            
 [97] BiocManager_1.30.10         data.table_1.13.6           cowplot_1.1.1              
[100] bitops_1.0-6                GenomicRanges_1.42.0        qvalue_2.22.0              
[103] R6_2.5.0                    gridExtra_2.3               MASS_7.3-53                
[106] assertthat_0.2.1            SummarizedExperiment_1.20.0 openssl_1.4.3              
[109] DESeq2_1.30.0               withr_2.4.1                 GenomeInfoDbData_1.2.4     
[112] hms_1.0.0                   grid_4.0.5                  rvcheck_0.1.8              
[115] MatrixGenerics_1.2.1        ggforce_0.3.3               lubridate_1.7.9.2
pathview • 383 views
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Entering edit mode

Progress

It looks like when fetching data from BioMart, some ensembl gene IDs produce multiple rows with the same entrez gene IDs. This could be part of the problem.

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1
Entering edit mode
Duncan • 0
@0e15754d
Last seen 15 months ago
South Africa

Solved

I found that setting cpd = c(1, 1) in the limit parameter sometimes crashed the render - this was due to the compound limits being set to the same value. Debugged by trawling through the code on GitHub until I found the error message

Beware! It seems that this fails silently sometimes!

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