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Mataivic
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@mataivic-12506
Last seen 7.6 years ago
Good morning,
I have a script using pathview in a shiny App for a project of my bioinformatics master degree. Everything worked well but suddendly, a couple of days ago, a bug came out of nowhere, without any code modification, when launching the pathview command :
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, : unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type)) Warning: Error in $<-.data.frame: replacement has 76 rows, data has 96 I copied and paste the code outside the shinyApp, and it worked again (the xml and png files went into my 'user/Documents/' directory. Then, on the second try, it bugged again ! And so on, one time it work, the second time it doesn't (in shiny, it never works). I have absolutely no idea why such a thing is happening.
It happened one or two weeks ago. The worst is that everything worked well and suddendly this bug came, without any code editing from me. I have a small script in order to figure that out, here it is :
library(clusterProfiler)
library(pathview)
inputfile=file.choose()
data <- read.table(inputfile, header=TRUE, dec=",")
#maybe you'll need to add sep="\t" or something like that
genes <- data$Ensembl_Gene_ID
EntrezIDs = bitr(genes, fromType= IdsType , toType="ENTREZID", OrgDb="org.Hs.eg.db")$ENTREZID
keggs=enrichKEGG(EntrezIDs ,pAdjustMethod="fdr", pvalueCutoff=0.01, qvalueCutoff=0.05)
# bug here
pathview(gene.data=EntrezIDs, pathway.id=as.matrix(as.data.frame(keggs)[1])[1:3],species="hsa", limit=c(1,3))
Here is the input file (shortened since I am limited to 15000 characters, I hope it won't messed up the results) :
Ensembl_Gene_ID Gene_Symbol log2FC p_value adj_pvalue ENSG00000090339 ICAM1 6,6698404077 0 0 ENSG00000108691 CCL2 6,3927430651 0 0 ENSG00000118503 TNFAIP3 4,1752383048 0 0 ENSG00000162692 VCAM1 9,0516122689 0 0 ENSG00000185215 TNFAIP2 3,3128766885 0 0 ENSG00000169429 IL8 3,4854038547 1,49E-291 4,76E-288 ENSG00000077150 NFKB2 3,6760936413 9,72E-277 2,82E-273 ENSG00000100906 NFKBIA 2,8107738915 1,69E-238 4,50E-235 ENSG00000161011 SQSTM1 1,404984023 6,60E-87 3,91E-84 ENSG00000164251 F2RL1 2,228720453 7,80E-174 1,25E-170 ENSG00000145365 TIFA 2,4827316786 9,05E-190 1,61E-186 ENSG00000056558 TRAF1 4,3219219715 0 0 ENSG00000104856 RELB 5,3740452546 0 0 ENSG00000007908 SELE 6,5992071817 0 0 ENSG00000023445 BIRC3 7,1013231569 0 0 ENSG00000128284 APOL3 3,0580886345 5,34E-219 1,31E-215 ENSG00000184371 CSF1 2,8747119649 1,34E-200 2,51E-197 ENSG00000160326 SLC2A6 2,371736578 7,25E-153 9,27E-150 ENSG00000112149 CD83 5,1849020913 6,25E-209 1,25E-205 ENSG00000169248 CXCL11 3,9885010193 3,59E-153 4,78E-150 ENSG00000163735 CXCL5 5,3189628206 6,02E-161 8,75E-158 ENSG00000006210 CX3CL1 6,2047905222 2,06E-142 2,53E-139 ENSG00000185101 ANO9 5,5319492083 6,65E-119 6,25E-116 ENSG00000227507 LTB 4,5693401008 8,35E-99 5,93E-96 ENSG00000086061 DNAJA1 0,6160659876 8,81E-20 1,04E-17 ENSG00000145632 PLK2 0,3743843813 3,41E-08 1,54E-06 ENSG00000137575 SDCBP 0,5110720979 1,04E-13 8,15E-12 ENSG00000185551 NR2F2 -0,4961472049 2,83E-13 2,15E-11 ENSG00000143878 RHOB 0,3760342184 1,01E-07 4,24E-06 ENSG00000163661 PTX3 0,7264569628 3,04E-18 3,32E-16 ENSG00000143321 HDGF 0,3691856958 2,76E-07 1,08E-05 ENSG00000166710 B2M 0,546357382 2,92E-12 2,01E-10 ENSG00000091527 CDV3 0,3818032113 4,70E-08 2,08E-06 ENSG00000167996 FTH1 0,2597510103 0,0013737609 0,0215751345 ENSG00000104951 IL4I1 3,4292833296 1,11E-140 1,27E-137 ENSG00000142871 CYR61 0,2496820627 0,0001860959 0,0039336139 ENSG00000172602 RND1 3,1459477897 1,09E-128 1,12E-125 ENSG00000008517 IL32 2,6720847487 6,15E-172 9,36E-169 ENSG00000049249 TNFRSF9 8,1430466274 1,04E-105 8,28E-103 ENSG00000188015 S100A3 4,0520465746 6,83E-108 5,60E-105 ENSG00000163739 CXCL1 3,2317419311 2,29E-210 4,88E-207 ENSG00000110848 CD69 3,9921576403 5,45E-104 4,15E-101 ENSG00000164932 CTHRC1 1,8587056384 4,35E-105 3,39E-102 ENSG00000124875 CXCL6 3,5080734691 2,70E-188 4,54E-185 ENSG00000115919 KYNU 3,8834279178 1,61E-103 1,20E-100 ENSG00000115009 CCL20 5,9380301295 1,03E-111 8,85E-109 ENSG00000159840 ZYX 0,221308813 0,0017025307 0,0255678561 ENSG00000234745 HLA-B 2,2802098006 8,97E-113 8,19E-110 ENSG00000160223 ICOSLG 3,4416028095 1,03E-218 2,34E-215 ENSG00000163545 NUAK2 3,2891894371 7,64E-96 4,98E-93 ENSG00000169245 CXCL10 8,4054198187 1,83E-94 1,17E-91 ENSG00000069493 CLEC2D 3,5342574865 1,45E-78 7,74E-76 ENSG00000204592 HLA-E 0,616047908 1,69E-15 1,49E-13 ENSG00000145901 TNIP1 2,0278859147 5,11E-158 7,11E-155 ENSG00000104312 RIPK2 1,48650534 3,65E-82 2,12E-79 ENSG00000123240 OPTN 1,7975448821 8,58E-123 8,57E-120 ENSG00000253522 MIR146A 3,3553807205 2,68E-72 1,28E-69 ENSG00000168394 TAP1 2,102288878 1,51E-131 1,61E-128 ENSG00000146232 NFKBIE 2,3570285443 3,87E-112 3,44E-109 ENSG00000205502 C2CD4B 2,9440001323 6,26E-74 3,18E-71 ENSG00000167100 SAMD14 1,9532366462 6,55E-69 2,91E-66 ENSG00000113504 SLC12A7 1,4720046424 9,48E-80 5,22E-77 ENSG00000100401 RANGAP1 0,6857346473 6,76E-20 8,09E-18 ENSG00000100767 PAPLN 2,3421900636 1,39E-78 7,52E-76 ENSG00000058085 LAMC2 1,5431664983 2,86E-53 1,04E-50 ENSG00000270607 RP11-359E10.1 2,3854036344 1,47E-70 6,72E-68 ENSG00000107201 DDX58 1,4595388552 1,70E-73 8,48E-71 ENSG00000081041 CXCL2 3,0262033543 7,41E-43 2,09E-40 ENSG00000163132 MSX1 2,7761598722 1,29E-66 5,51E-64 ENSG00000028277 POU2F2 2,0466146728 3,97E-65 1,65E-62 ENSG00000050730 TNIP3 3,229329092 1,37E-44 4,10E-42 ENSG00000128335 APOL2 1,473090214 2,09E-70 9,41E-68 ENSG00000237988 OR2I1P 7,8419334093 3,18E-67 1,37E-64 ENSG00000105246 EBI3 5,0935025027 1,23E-59 4,89E-57 ENSG00000124145 SDC4 1,407771963 6,90E-76 3,55E-73 ENSG00000115267 IFIH1 2,6863181071 9,94E-139 1,10E-135 ENSG00000112096 SOD2 1,7840242915 7,44E-121 7,21E-118 ENSG00000126561 STAT5A 1,382924375 6,59E-72 3,10E-69 ENSG00000144476 ACKR3 1,5463153496 1,10E-43 3,14E-41 ENSG00000132481 TRIM47 1,8400193127 3,47E-94 2,17E-91 ENSG00000115604 IL18R1 1,7758792324 4,38E-102 3,18E-99 ENSG00000064042 LIMCH1 -1,697667608 1,06E-57 4,09E-55 ENSG00000075223 SEMA3C 2,6428794379 4,87E-34 1,04E-31 ENSG00000271856 RP11-861A13.4 5,3162419344 7,11E-64 2,91E-61 ENSG00000107282 APBA1 -1,4667390864 1,85E-36 4,38E-34 ENSG00000163131 CTSS 2,6929454478 4,65E-111 3,91E-108 ENSG00000120337 TNFSF18 1,5716255441 8,91E-90 5,48E-87 ENSG00000166387 PPFIBP2 -1,3608246629 7,19E-36 1,62E-33 ENSG00000213859 KCTD11 1,0580714969 1,04E-23 1,52E-21 ENSG00000085831 TTC39A 2,4578133228 9,15E-25 1,41E-22 ENSG00000163513 TGFBR2 0,4969789653 3,46E-09 1,81E-07 ENSG00000139174 PRICKLE1 -1,4142683759 3,02E-73 1,48E-70 ENSG00000184530 C6orf58 6,0201724937 1,58E-51 5,42E-49 ENSG00000179862 CITED4 1,3708051503 1,16E-22 1,59E-20 ENSG00000115008 IL1A 2,6593891142 7,46E-43 2,09E-40 ENSG00000131037 EPS8L1 1,0947789046 4,79E-20 5,76E-18 ENSG00000117228 GBP1 1,2025593197 6,13E-52 2,15E-49 ENSG00000172738 TMEM217 1,9639810453 3,00E-54 1,10E-51 ENSG00000168314 MOBP 2,4845110741 2,38E-26 3,92E-24 ENSG00000134070 IRAK2 2,2955364885 2,08E-141 2,46E-138 ENSG00000198535 C2CD4A 4,577996172 1,20E-40 3,24E-38 ENSG00000163874 ZC3H12A 0,9381369244 1,78E-18 1,98E-16 ENSG00000185291 IL3RA 2,3420467737 8,82E-44 2,54E-41 ENSG00000105639 JAK3 2,495057148 1,52E-41 4,18E-39 ENSG00000171223 JUNB 2,0335078068 5,12E-81 2,87E-78 ENSG00000163347 CLDN1 2,4949072106 1,73E-27 2,96E-25 ENSG00000181656 GPR88 2,0975113695 4,44E-25 6,99E-23 ENSG00000164136 IL15 2,2652411451 6,11E-47 1,90E-44 ENSG00000178695 KCTD12 -0,7539496907 7,25E-23 9,98E-21 ENSG00000176907 C8orf4 1,6829692594 1,49E-81 8,50E-79 ENSG00000163734 CXCL3 3,0321033172 4,77E-32 9,58E-30 ENSG00000185022 MAFF 1,3309075932 1,13E-46 3,49E-44 ENSG00000163840 DTX3L 1,2171662272 6,27E-38 1,55E-35 ENSG00000240065 PSMB9 2,2505005445 4,07E-35 8,98E-33 ENSG00000204642 HLA-F 2,1177972557 2,64E-22 3,53E-20 ENSG00000125347 IRF1 1,4482064145 8,65E-58 3,37E-55 ENSG00000162772 ATF3 1,4948349223 4,86E-33 1,00E-30 ENSG00000027697 IFNGR1 1,0231240904 2,49E-36 5,76E-34 ENSG00000171408 PDE7B -1,169170306 1,73E-29 3,09E-27 ENSG00000168685 IL7R 2,125882044 2,32E-96 1,55E-93 ENSG00000177409 SAMD9L 1,2162404685 5,73E-32 1,14E-29 ENSG00000136560 TANK 1,1525846708 7,03E-51 2,34E-48 ENSG00000109320 NFKB1 1,5459523059 6,58E-87 3,91E-84 ENSG00000139263 LRIG3 1,2088786453 2,15E-62 8,69E-60 ENSG00000161940 BCL6B 1,1369814172 6,66E-51 2,24E-48 ENSG00000108984 MAP2K6 -1,378263906 1,92E-39 4,90E-37 ENSG00000132109 TRIM21 1,0587983659 4,22E-36 9,62E-34 ENSG00000136490 LIMD2 1,1414650881 2,93E-31 5,74E-29 ENSG00000169403 PTAFR 2,166927154 6,16E-21 7,66E-19 ENSG00000128274 A4GALT 0,9518357944 6,31E-14 5,03E-12 ENSG00000083799 CYLD 1,210521761 2,05E-42 5,70E-40 ENSG00000168310 IRF2 1,2216681724 4,91E-47 1,54E-44 ENSG00000012211 PRICKLE3 0,9224797711 1,10E-15 9,98E-14 ENSG00000121858 TNFSF10 1,6268549998 2,36E-58 9,33E-56 ENSG00000111339 ART4 1,1092601697 4,43E-36 1,00E-33 ENSG00000119917 IFIT3 1,426688259 6,75E-31 1,29E-28 ENSG00000110446 SLC15A3 2,1584288816 1,45E-33 3,05E-31 ENSG00000171608 PIK3CD 1,2125359085 8,36E-40 2,17E-37 ENSG00000143387 CTSK 1,6805693689 1,85E-49 5,96E-47 ENSG00000168961 LGALS9 1,1324240248 3,44E-13 2,59E-11 ENSG00000197951 ZNF71 0,967458386 3,97E-23 5,59E-21 ENSG00000135736 CCDC102A 1,0619472932 9,57E-18 1,02E-15 ENSG00000162654 GBP4 2,502767742 1,02E-97 7,09E-95 ENSG00000164342 TLR3 1,0648394078 1,68E-16 1,62E-14 ENSG00000117226 GBP3 1,1214295893 2,49E-47 7,88E-45 ENSG00000178726 THBD -1,4528817816 3,55E-25 5,62E-23 ENSG00000214530 STARD10 1,5633072958 1,11E-38 2,78E-36 ENSG00000138678 AGPAT9 -1,1430936762 5,60E-32 1,12E-29 ENSG00000150048 CLEC1A 1,2751911972 7,72E-55 2,87E-52 ENSG00000231925 TAPBP 1,3480413157 1,26E-68 5,52E-66 ENSG00000133401 PDZD2 2,3248274849 7,95E-40 2,08E-37 ENSG00000178078 STAP2 1,28193951 3,40E-23 4,80E-21 ENSG00000135932 CAB39 0,9256585597 1,46E-35 3,26E-33 ENSG00000159128 IFNGR2 0,9511059149 1,21E-34 2,61E-32 ENSG00000213886 UBD 7,6186044178 3,41E-22 4,51E-20 ENSG00000143457 GOLPH3L 0,9607766432 1,80E-39 4,63E-37 ENSG00000173391 OLR1 7,7114015901 5,57E-23 7,71E-21 ENSG00000156587 UBE2L6 0,8515373492 1,57E-16 1,53E-14 ENSG00000272269 RP11-500C11.3 1,6678950328 4,05E-66 1,70E-63 ENSG00000267607 CTD-2369P2.8 7,4805566417 1,05E-20 1,30E-18 ENSG00000010030 ETV7 3,5462544329 2,05E-25 3,29E-23 ENSG00000178038 ALS2CL 0,7803985197 1,34E-12 9,59E-11 ENSG00000154639 CXADR -1,0564152322 1,54E-29 2,77E-27 ENSG00000165801 ARHGEF40 1,4957938646 1,09E-51 3,79E-49 ENSG00000171227 TMEM37 -1,9016765305 1,14E-16 1,12E-14 ENSG00000145779 TNFAIP8 1,2349523996 1,40E-55 5,28E-53 ENSG00000162616 DNAJB4 -0,6648872946 1,48E-19 1,73E-17 ENSG00000132530 XAF1 1,0866278536 9,62E-23 1,32E-20 ENSG00000130589 HELZ2 1,2062416729 8,37E-46 2,52E-43 ENSG00000119922 IFIT2 1,6562895595 2,72E-16 2,58E-14 ENSG00000152689 RASGRP3 1,2913579655 9,56E-31 1,82E-28 ENSG00000154721 JAM2 2,7582655566 1,60E-23 2,30E-21 ENSG00000124212 PTGIS 1,3607275428 7,75E-29 1,35E-26 ENSG00000125898 FAM110A 0,7699331901 5,45E-11 3,40E-09 ENSG00000132003 ZSWIM4 1,7616984729 1,40E-72 6,76E-70 ENSG00000153721 CNKSR3 1,581266048 8,85E-39 2,23E-36 ENSG00000119714 GPR68 1,6813999238 1,50E-15 1,35E-13 ENSG00000163121 NEURL3 4,8947295863 2,82E-18 3,10E-16 ENSG00000204261 TAPSAR1 1,7286495357 2,63E-22 3,53E-20 ENSG00000152784 PRDM8 1,3177095327 2,45E-23 3,50E-21 ENSG00000155130 MARCKS 0,3369290495 4,18E-07 1,60E-05 ENSG00000149212 SESN3 -0,9948166535 7,71E-13 5,65E-11 ENSG00000100368 CSF2RB 1,0499093721 5,70E-33 1,17E-30 ENSG00000143466 IKBKE 1,1726116768 3,24E-48 1,04E-45 ENSG00000167207 NOD2 4,1387725935 8,46E-24 1,26E-21 ENSG00000100678 SLC8A3 5,436416856 9,64E-17 9,51E-15 ENSG00000169085 C8orf46 3,9179192668 7,17E-28 1,23E-25 ENSG00000196776 CD47 1,0211094014 8,26E-44 2,40E-41 ENSG00000102934 PLLP 1,7574549603 3,20E-37 7,74E-35 ENSG00000160190 SLC37A1 0,8662438352 9,61E-17 9,51E-15 ENSG00000167191 GPRC5B 1,3510883965 5,59E-51 1,90E-48 ENSG00000178882 FAM101A 1,0828435301 1,93E-39 4,90E-37 ENSG00000104825 NFKBIB 0,8083231505 7,72E-22 1,01E-19 ENSG00000119801 YPEL5 0,8034326357 4,90E-26 8,03E-24 ENSG00000181634 TNFSF15 1,4304497633 2,37E-37 5,79E-35 ENSG00000129667 RHBDF2 1,1649981551 6,94E-44 2,05E-41 ENSG00000184602 SNN 0,7740862573 1,48E-20 1,81E-18
I'm probably too late for this specific issue, but I just ran into a similar problem. If I run the example from the pathview vignette:
Everything works fine.
But if I also load the package mixOmics the example code breaks:
library(mixOmics) library(pathview) library(gage) data("gse16873") cn <- colnames(gse16873) hn <- grep('HN',cn, ignore.case =TRUE) dcis <- grep('DCIS',cn, ignore.case =TRUE) data(kegg.gs) gse16873.kegg.p <- gage(gse16873, gsets = kegg.gs,ref=hn,samp=dcis) gse16873.d <- gagePrep(gse16873, ref = hn, samp = dcis) gse16873.d <- gse16873[,dcis]-gse16873[,hn] sel <- gse16873.kegg.p$greater[, "q.val"] < 0.1 & !is.na(gse16873.kegg.p$greater[,'q.val']) path.ids <- rownames(gse16873.kegg.p$greater)[sel] path.ids2 <- substr(path.ids[c(1, 2, 7)], 1, 8) pv.out.list <- sapply(path.ids2, function(pid) pathview(gene.data = gse16873.d[,1:2], pathway.id = pid, species = "hsa")) Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, : unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type)) Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", : replacement has 86 rows, data has 99So maybe there is some kind of namespace issue?
Here are the sessionInfos.
This works:This does not:
This is more likely due to shiny as discussed in the main thread. Note shiny is also loaded in your second sessionInfo. Again the best way is not to load shiny, or use use the pathview web server:
https://pathview.uncc.edu/