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Question: Pathview pathview kegg.native=TRUE throws error in img
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gravatar for guillermo.marco
7 months ago by
Spain
guillermo.marco20 wrote:

I'm trying to retrieve some native from KEGG using pathview. However I'm experiencing an error with a specific pathway that I'm not able to debug or solve. I've been able to retrieve other pathways with different pathway.id without any problem. However "hsa04215" is failing, I would like to know if there's any way to fix this behavior.

pathview(gene.data  = genes_vector,
         pathway.id = "hsa04215",
         species    = "hsa",
         out.suffix = "KEGG_native",
         kegg.native = TRUE)
 
'select()' returned 1:1 mapping between keys and columns:
Working in directory /tmp
Info: Writing image file hsa04215.KEGG_native.png
Info: some node width is different from others, and hence adjusted!
Error in img[pidx[i, 3]:pidx[i, 4], sel.px, 1:3] :  only 0's may be mixed with negative subscripts
> genes_vector
     9625     10060      2180    222487       133     51327      9447       249       306     91056       366    151516     10409    116071       597       598 
 1.570238 -2.755893  1.763372  1.566436  2.139035 -2.309179  2.260622  1.815560  1.853472  1.530103  1.835312  1.561068  1.602145  1.842875  1.642464 -1.544459 
      332       660       669       671     79908       699    132720       762       820       838       891      9133      1230     57126     29126       947 
 1.801568  1.804063 -1.611295 -2.051103  1.833427  1.663747 -1.634926  2.004274 -1.654111  2.279283  1.585199  1.593752  1.616503  3.712137  1.849766 -3.438811 
   157313    113130     55143       983      1084      1088     55165    338339     26253     64581      9586     10321     83716      1511      3627      3577 
 2.051274  1.903135  1.695892  1.735429  1.792758 -2.775870  1.735046  1.792087  1.555376  1.573478  1.812016 -2.696672  1.814243 -2.772332 -2.219093  1.884709 
     3579     55601     91351      1668      1669     84649      9787      9732      1823      8291      1870      5610      2048     94240      2150    116151 
 1.799154  1.725846  1.521301 -2.825742 -2.222279  1.577899  1.786686  1.911808 -1.730132  1.585822  2.204055  1.653056  2.614147  2.004483  1.603913 -1.681992 
    25793      8857      9638      2867      2352      2357      9846     79623      2633     25801      2766     51512      2994      3039      3040    338442 
-1.614782 -1.582182 -1.984923  1.691381  2.038390  1.642650  1.534744  2.677414  1.619135  1.587386 -1.526761  1.792883 -3.544126 -1.809089 -1.866683  1.503426 
     8843     55363     51191     55008      3161      3310      3429     10561     10964      2537     24138     10410 100423062      7850      9636     55600 
 1.634949 -1.721534  1.968032  1.688094  1.863056  1.597617 62.416692  4.514543  6.150356  1.974234  1.666593  2.222233  1.598270  1.870946  1.537554 -2.532373 
     3512      3772      3759     11004    113730     83999     25984      3902     27074      3934      9079      8825      4000    116844    120892      4057 
 2.130778  1.970473  1.971387  1.687145  2.146684  2.279883  1.842663  2.620932  2.337636 -2.268093 -1.994046  1.513246 -1.561817  1.756087  1.525764 -3.133402 
     4061     23643     54682     55388      4222     93432      4311     64386      4317      4318     51338      4481      4599      4084      4635     10135 
 1.973927  1.519471  1.851248  2.090546 -1.805691  1.834323  1.976355  1.610107 -2.048560  2.076840  1.887559  1.779113  1.929767  1.669332 -1.651886  1.832429 
     4734      4751    389643     51203      4938      4939      4940      8638     10562      4973      9381     11240      9260      5266      5347      5359 
-2.388840  2.001109  1.983099  1.611863  1.763180  1.578838  2.739305  1.980315 -2.979913 -2.451628 16.915102  1.559154  1.575523  2.003163  1.586417  1.889634 
    79660     60675     79056      5743     25797     57111    158158      5997     11237      6241     91543      6285      8578      8991      5414       710 
 1.778012  2.147265  1.694335  1.559004  1.562877 -2.147935 -2.736478  1.600540  1.543364  2.050762  3.249528 -2.101734  1.662271 -2.070530  1.790653  3.036586 
    79801    729993    283514      6614    220134      6563     51629    116369      6515      6521      6622      9021     26010     55437      6809      7083 
 1.735148 -2.007027 -1.995227  6.345835  1.990659 -1.570262 -1.529665  3.535784  1.598581 -2.454552 -2.094840  1.554689  2.396236 -1.810107  1.561795  1.716731 
     7100    130827     55076      7130       608     10673      7145      7153     51673     22974      7280     81567     11065     11274      8876      8875 
 1.599068 -2.178371 -2.254848  2.470752  1.557093  1.530946 -1.714608  1.847099 -1.903531  1.601103 -1.972150  1.655575  1.758149  2.155138  1.757706  1.750470 
    55350     79819     54739      8531     27033     54877 
 1.609773 -2.314627  1.927417 -1.664515  2.183920  1.694940 

 

Session info:

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

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  
[6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GOSemSim_2.0.4         plyr_1.8.4             openxlsx_4.0.4         rtracklayer_1.34.2     GenomicRanges_1.26.3   GenomeInfoDb_1.10.3  
[7] pathview_1.14.0        org.Hs.eg.db_3.4.0     AnnotationDbi_1.36.2   IRanges_2.8.1          S4Vectors_0.12.1       Biobase_2.34.0       
[13] AnnotationHub_2.6.4    BiocGenerics_0.20.0    clusterProfiler_3.2.11 DOSE_3.0.10            optparse_1.3.2        

loaded via a namespace (and not attached):
[1] KEGGgraph_1.32.0              Rcpp_0.12.9.2                 lattice_0.20-34               GO.db_3.4.0                   tidyr_0.6.1                 
[6] png_0.1-7                     Rsamtools_1.26.1              Biostrings_2.42.1             assertthat_0.1                digest_0.6.12               
[11] mime_0.5                      R6_2.2.0                      RSQLite_1.1-2                 httr_1.2.1                    ggplot2_2.2.1               
[16] BiocInstaller_1.24.0          zlibbioc_1.20.0               lazyeval_0.2.0                data.table_1.10.4             Rgraphviz_2.18.0            
[21] Matrix_1.2-8                  qvalue_2.6.0                  splines_3.3.2                 BiocParallel_1.8.1            stringr_1.2.0               
[26] igraph_1.0.1                  RCurl_1.95-4.8                munsell_0.4.3                 shiny_1.0.0                   fgsea_1.0.2                 
[31] httpuv_1.3.3                  htmltools_0.3.5               SummarizedExperiment_1.4.0    KEGGREST_1.14.0               tibble_1.2                  
[36] gridExtra_2.2.1               interactiveDisplayBase_1.12.0 XML_3.98-1.3                  dplyr_0.5.0                   GenomicAlignments_1.10.0    
[41] bitops_1.0-6                  grid_3.3.2                    xtable_1.8-2                  gtable_0.2.0                  DBI_0.5-1                   
[46] magrittr_1.5                  scales_0.4.1                  graph_1.52.0                  stringi_1.1.2                 XVector_0.14.0              
[51] reshape2_1.4.2                getopt_1.20.0                 DO.db_2.9                     fastmatch_1.1-0               yaml_2.1.14                 
[56] colorspace_1.3-2              memoise_1.0.0 
ADD COMMENTlink modified 7 months ago by Luo Weijun1.4k • written 7 months ago by guillermo.marco20
0
gravatar for Luo Weijun
7 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Does this error only occur to pathway 04215 or other pathways too, only with this data or other data too?
ADD COMMENTlink written 7 months ago by Luo Weijun1.4k

I've experienced this issue with other pathways too. I can't enumerate them because I don't have logs.

ADD REPLYlink written 6 months ago by guillermo.marco20
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