Error in img[pidx[i, 3]:pidx[i, 4], sel.px, 1:3] : only 0's may be mixed with negative subscripts

[ErickMUO]

Hi, pathway view developers!

I was using your package and it works smoothly. However, for some pathways, there is a strange error.

I am using the following command:
n; represents the number of the pathway I am interested in:
hsa04550 Work well
hsa04261 Work well
hsa04630 Work well
hsa01230 NO RESULTS
hsa05206 NO RESULTS
hsa04115 Work well
hsa02010 Work well
hsa01100 NO RESULTS

hsan <- pathview(gene.data = result_vector_DE_entrezlogFC1,
pathway.id = "hsan",
species = "hsa",
limit = list(gene=max(abs(result_vector_DE_entrezlogFC1)), cpd=1))

Error in img[pidx[i, 3]:pidx[i, 4], sel.px, 1:3] : only 0's may be mixed with negative subscripts

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Stockholm
tzcode source: internal

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

other attached packages:
[1] pathview_1.40.0 enrichplot_1.20.0 clusterProfiler_4.8.1
[4] WebGestaltR_0.4.6 pheatmap_1.0.12 org.Hs.eg.db_3.17.0
[7] AnnotationDbi_1.62.1 EnhancedVolcano_1.18.0 ggrepel_0.9.3
[10] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[13] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[16] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[19] tidyverse_2.0.0 DESeq2_1.40.1 SummarizedExperiment_1.30.2
[22] Biobase_2.60.0 MatrixGenerics_1.12.0 matrixStats_1.0.0
[25] GenomicRanges_1.52.0 GenomeInfoDb_1.36.0 IRanges_2.34.0
[28] S4Vectors_0.38.1 BiocGenerics_0.46.0 tximport_1.28.0
[31] biomaRt_2.56.1

loaded via a namespace (and not attached):
[1] later_1.3.1 splines_4.3.0 urltools_1.7.3
[4] bitops_1.0-7 ggplotify_0.1.0 filelock_1.0.2
[7] triebeard_0.4.1 polyclip_1.10-4 preprocessCore_1.62.1
[10] graph_1.78.0 XML_3.99-0.14 lifecycle_1.0.3
[13] doParallel_1.0.17 vroom_1.6.3 lattice_0.21-8
[16] MASS_7.3-60 magrittr_2.0.3 limma_3.56.2
[19] yaml_2.3.7 httpuv_1.6.11 doRNG_1.8.6
[22] cowplot_1.1.1 DBI_1.1.3 RColorBrewer_1.1-3
[25] zlibbioc_1.46.0 ggraph_2.1.0 RCurl_1.98-1.12
[28] yulab.utils_0.0.6 tweenr_2.0.2 rappdirs_0.3.3
[31] GenomeInfoDbData_1.2.10 tidytree_0.4.2 reactome.db_1.84.0
[34] svglite_2.1.1 codetools_0.2-19 DelayedArray_0.26.3
[37] DOSE_3.26.1 xml2_1.3.4 ggforce_0.4.1
[40] tidyselect_1.2.0 aplot_0.1.10 farver_2.1.1
[43] viridis_0.6.3 BiocFileCache_2.8.0 jsonlite_1.8.5
[46] ellipsis_0.3.2 tidygraph_1.2.3 ggridges_0.5.4
[49] iterators_1.0.14 systemfonts_1.0.4 foreach_1.5.2
[52] bbmle_1.0.25 ggnewscale_0.4.9 tools_4.3.0
[55] progress_1.2.2 treeio_1.24.1 ragg_1.2.5
[58] Rcpp_1.0.10 glue_1.6.2 gridExtra_2.3
[61] qvalue_2.32.0 withr_2.5.0 numDeriv_2016.8-1.1
[64] BiocManager_1.30.21 fastmap_1.1.1 rhdf5filters_1.12.1
[67] fansi_1.0.4 digest_0.6.31 mime_0.12
[70] timechange_0.2.0 R6_2.5.1 gridGraphics_0.5-1
[73] textshaping_0.3.6 colorspace_2.1-0 GO.db_3.17.0
[76] RSQLite_2.3.1 utf8_1.2.3 generics_0.1.3
[79] data.table_1.14.8 prettyunits_1.1.1 graphlayouts_1.0.0
[82] httr_1.4.6 S4Arrays_1.0.4 scatterpie_0.2.1
[85] whisker_0.4.1 graphite_1.46.0 pkgconfig_2.0.3
[88] gtable_0.3.3 progeny_1.22.0 blob_1.2.4
[91] XVector_0.40.0 htmltools_0.5.5 shadowtext_0.1.2
[94] fgsea_1.26.0 scales_1.2.1 png_0.1-8
[97] ggfun_0.0.9 rstudioapi_0.14 tzdb_0.4.0
[100] reshape2_1.4.4 coda_0.19-4 nlme_3.1-162
[103] curl_5.0.1 bdsmatrix_1.3-6 cachem_1.0.8
[106] rhdf5_2.44.0 BiocVersion_3.17.1 parallel_4.3.0
[109] HDO.db_0.99.1 vsn_3.68.0 apeglm_1.22.1
[112] ReactomePA_1.44.0 pillar_1.9.0 grid_4.3.0
[115] vctrs_0.6.3 promises_1.2.0.1 dbplyr_2.3.2
[118] xtable_1.8-4 Rgraphviz_2.44.0 KEGGgraph_1.60.0
[121] mvtnorm_1.2-2 cli_3.6.1 locfit_1.5-9.8
[124] compiler_4.3.0 rngtools_1.5.2 rlang_1.1.1
[127] crayon_1.5.2 MeSHDbi_1.36.0 labeling_0.4.2
[130] emdbook_1.3.12 affy_1.78.0 plyr_1.8.8
[133] stringi_1.7.12 viridisLite_0.4.2 BiocParallel_1.34.2
[136] munsell_0.5.0 Biostrings_2.68.1 lazyeval_0.2.2
[139] GOSemSim_2.26.0 Matrix_1.5-4.1 europepmc_0.4.1
[142] hms_1.1.3 patchwork_1.1.2 bit64_4.0.5
[145] Rhdf5lib_1.22.0 shiny_1.7.4 KEGGREST_1.40.0
[148] interactiveDisplayBase_1.38.0 AnnotationHub_3.8.0 apcluster_1.4.10
[151] igraph_1.5.0 memoise_2.0.1 affyio_1.70.0
[154] ggtree_3.8.0 fastmatch_1.1-3 bit_4.0.5
[157] downloader_0.4 ape_5.7-1 gson_0.1.0

[raw937]

Are you still having this issue?

If you have the same issues place in: https://github.com/Kannapolis-Bioinformatics/pathview/issues
We can answer your question?

many thanks,
Rick

[ErickMUO]

Hi Rick,

I have retried running the problematic pathways, and it seems that the error has changed. I will now post the new error on the GitHub repository you provided. For me, it seems that is due to the complexity of the pathway. Since the problematic ones are the more crowded but who knows..

Regards

[Luli227]

Hi Rick,

I have retried running the problematic pathways, and it seems that the error has changed. I will now post the new error on the GitHub repository you provided. For me, it seems that is due to the complexity of the pathway. Since the problematic ones are the more crowded but who knows..

Regards

Hi,Erick,

I'm having the same issue as you. It also shows"Error in img[pidx[i, 3]:pidx[i, 4], sel.px, 1:3] : only 0's may be mixed with negative subscripts",I find many methods but they are false,Can you tell me how you did it？

Many thanks,
Yuan

[ErickMUO]

Hi Luli227,

I tried to reproduce the previously reported error, but after updating the pathview package to version 1.42.0, the issue no longer persists. I am currently using the package without encountering the mentioned error. Regrettably, I couldn't offer additional help this time. However, the details of how I initially encountered the error are provided at the beginning of this thread.