Pathview pathview kegg.native=TRUE throws error in img
2
1
Entering edit mode
@guillermomarco-11336
Last seen 7.1 years ago
Spain

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 
pathview kegg error bioconductor rnaseq • 2.2k views
ADD COMMENT
0
Entering edit mode
Luo Weijun ★ 1.6k
@luo-weijun-1783
Last seen 9 months ago
United States
Does this error only occur to pathway 04215 or other pathways too, only with this data or other data too?
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
map2085 ▴ 40
@map2085-9227
Last seen 5.9 years ago
United States

I have same problem

ADD COMMENT

Login before adding your answer.

Traffic: 623 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6