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