Error with term_gene_heatmap and UpSet_plot

[cristanchoa]

Hi, Thank you for such a great program. I was able to obtain enrichment pathway information (output_df) with my dataset (input_df). However, when I try to use term_gene_heatmap() and UpSet_plot() I get the following error: "Error in input_testing(genes_df) : p values must all be numeric."

I have opened it multiple times and the p values are numeric (example below). This is also the same samples I ran to get the enrichment, so it was able to pick up the p values then. Please let me know if there is anything I am missing.

Thank you, Ana

input_df: GENE CHANGE P_VALUE

1 P4ha1 -0.952 1e-13 2 Xpo1 -0.958 1e-13 3 Stmn4 -0.685 1e-13 4 Kdm3a -0.615 1e-13 RSession R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.2 (Ootpa) Matrix products: default BLAS: /cm/shared/apps_chop/R/4.0.5/lib64/R/lib/libRblas.so LAPACK: /cm/shared/apps_chop/R/4.0.5/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.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] stats graphics grDevices utils datasets methods base other attached packages: [1] magrittr_2.0.1 pixmap_0.4-12 magick_2.7.2 future.callr_0.6.1 [5] future_1.21.0 callr_3.7.0 pak_0.1.2.1 pathfindR_1.6.1 [9] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 [13] readr_2.0.0 tidyr_1.1.3 tibble_3.1.3 ggplot2_3.3.5 [17] tidyverse_1.3.1 msigdbr_7.4.1 readxl_1.3.1 pathfindR.data_1.1.1 loaded via a namespace (and not attached): [1] colorspace_2.0-2 ellipsis_0.3.2 class_7.3-18 modeltools_0.2-23 [5] mclust_5.4.7 fs_1.5.0 rstudioapi_0.13 listenv_0.8.0 [9] farver_2.1.0 graphlayouts_0.7.1 ggrepel_0.9.1 flexmix_2.3-17 [13] bit64_4.0.5 fansi_0.5.0 lubridate_1.7.10 xml2_1.3.2 [17] codetools_0.2-18 R.methodsS3_1.8.1 doParallel_1.0.16 robustbase_0.93-8 [21] knitr_1.33 polyclip_1.10-0 jsonlite_1.7.2 rematch_1.0.1 [25] broom_0.7.9 cluster_2.1.1 kernlab_0.9-29 dbplyr_2.1.1 [29] R.oo_1.24.0 ggforce_0.3.3 compiler_4.0.5 httr_1.4.2 [33] backports_1.2.1 assertthat_0.2.1 cli_3.0.1 tweenr_1.0.2 [37] htmltools_0.5.1.1 tools_4.0.5 igraph_1.2.6 gtable_0.3.0 [41] glue_1.4.2 tinytex_0.33 Rcpp_1.0.7 cellranger_1.1.0 [45] vctrs_0.3.8 babelgene_21.4 iterators_1.0.13 fpc_2.2-9 [49] ggraph_2.0.5 xfun_0.25 globals_0.14.0 ps_1.6.0 [53] rvest_1.0.1 lifecycle_1.0.0 DEoptimR_1.0-9 MASS_7.3-53.1 [57] scales_1.1.1 tidygraph_1.2.0 vroom_1.5.4 hms_1.1.0 [61] parallel_4.0.5 gridExtra_2.3 stringi_1.7.3 foreach_1.5.1 [65] rlang_0.4.11 pkgconfig_2.0.3 prabclus_2.3-2 evaluate_0.14 [69] lattice_0.20-41 labeling_0.4.2 bit_4.0.4 tidyselect_1.1.1 [73] processx_3.5.2 parallelly_1.27.0 R6_2.5.0 generics_0.1.0 [77] DBI_1.1.1 pillar_1.6.2 haven_2.4.3 withr_2.4.2 [81] nnet_7.3-15 modelr_0.1.8 crayon_1.4.1 utf8_1.2.2 [85] tzdb_0.1.2 rmarkdown_2.10 viridis_0.6.1 grid_4.0.5 [89] reprex_2.0.1 digest_0.6.27 diptest_0.76-0 R.utils_2.10.1 [93] stats4_4.0.5 munsell_0.5.0 viridisLite_0.4.0 I'm working on a PC, but through a Redhat based HPC.

[egeulgen]

hey @cristanchoa,

Do you mind sharing the data frame you use (input_df) as an RDS file so that I can check for any issues?

Best, -E

[cristanchoa]

Hi,

Here it is!

Also, maybe germane to the problem, I can only get the initial enrichment analysis to work using what I think is the older version

input_processing(input = input, p_val_threshold = 0.05, pin_name_path = "mmu_STRING", convert2alias = FALSE)

I get the same problem when I try to use run_pathfindR Error in pathfindR::input_testing(input, p_val_threshold) : p values must all be numeric

Thanks in advance for your help! Ana

From: Ege Ulgen @.> Sent: Thursday, August 12, 2021 5:27 AM To: egeulgen/pathfindR @.> Cc: Cristancho, Ana G @.>; Mention @.> Subject: [External]Re: [egeulgen/pathfindR] Error with term_gene_heatmap and UpSet_plot (#94)

hey @cristanchoahttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcristanchoa&data=04%7C01%7CCristanchoA%40chop.edu%7C49d6311cee754ac3399b08d95d7355f3%7Ca611241607b041a59bb1d146b575c975%7C1%7C0%7C637643572239810825%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mwQzQbxt9z0jztvU58%2BYhqJu5KFFLK%2FjMbZAiH2t0vg%3D&reserved=0,

Do you mind sharing the data frame you use (input_df ) as an RDS file so that I can check for any issues?

Best, -E

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fegeulgen%2FpathfindR%2Fissues%2F94%23issuecomment-897486655&data=04%7C01%7CCristanchoA%40chop.edu%7C49d6311cee754ac3399b08d95d7355f3%7Ca611241607b041a59bb1d146b575c975%7C1%7C0%7C637643572239820819%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=K8qkO2oaskoWipSVMcYhtu1tCS04uoP4k85hloSpjyE%3D&reserved=0, or unsubscribehttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FASPDMCEK7BRNYO5W3QORMH3T4OHWBANCNFSM5B7IBSXQ&data=04%7C01%7CCristanchoA%40chop.edu%7C49d6311cee754ac3399b08d95d7355f3%7Ca611241607b041a59bb1d146b575c975%7C1%7C0%7C637643572239820819%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=5xVa5%2FSfj1e8%2FC7Pq0I4v%2F%2FIpT%2F%2FptiNN%2FGfBzSno80%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7CCristanchoA%40chop.edu%7C49d6311cee754ac3399b08d95d7355f3%7Ca611241607b041a59bb1d146b575c975%7C1%7C0%7C637643572239830813%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=CzqMmS7hb%2Bc58swXq1pEOr4RBgV4CNbzE2fQTpz3l1s%3D&reserved=0 or Androidhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26utm_campaign%3Dnotification-email&data=04%7C01%7CCristanchoA%40chop.edu%7C49d6311cee754ac3399b08d95d7355f3%7Ca611241607b041a59bb1d146b575c975%7C1%7C0%7C637643572239830813%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ln1adP%2BOqFj6Tr9k4ZTe1VO%2F4qAsn2MrvOvPR0B9pSQ%3D&reserved=0. This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker.

[egeulgen]

Hey @cristanchoa , The attachment isn’t there. I’m guessing your input is a tibble and that’s what causes the issue. Can you try running as.data.frame() first?

[cristanchoa]

Here goes again. I tested reloading it to my system. I think this should work. Thanks!

From: Ege Ulgen @.> Sent: Friday, August 13, 2021 12:15 PM To: egeulgen/pathfindR @.> Cc: Cristancho, Ana G @.>; Mention @.> Subject: [External]Re: [egeulgen/pathfindR] Error with term_gene_heatmap and UpSet_plot (#94)

Hey @cristanchoahttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcristanchoa&data=04%7C01%7CCristanchoA%40chop.edu%7C2bba2ee51bb54cc04fce08d95e758df8%7Ca611241607b041a59bb1d146b575c975%7C1%7C0%7C637644681268923087%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dnG48xvTxAuTST6BF74ykxaM27MUHz7w4fo6jct74nk%3D&reserved=0 , The attachment isn't there. I'm guessing your input is a tibble and that's what causes the issue. Can you try running as.data.frame() first?

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[cristanchoa]

I see what you mean now. Yes, all the commands now work when I process use as.data.frame() on the initial file. Thank you!!