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Question: Error in pathview - came out of nowhere without any source code modification
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gravatar for Mataivic
5 weeks ago by
Mataivic0
Mataivic0 wrote:

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

ADD COMMENTlink modified 29 days ago by Luo Weijun1.4k • written 5 weeks ago by Mataivic0
0
gravatar for Luo Weijun
29 days ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
not sure what’s the problem. I tried your data with the following code, it worked well. Note that pathview() function works with different gene ID types, Entrez, Ensembl Gene, Symbol etc. you don’t need to do ID conversion using bitr() function. inputfile="inputfile.txt" my.data=read.delim(inputfile, header=TRUE, dec=",",sep=" ") my.data=my.data[,c(1,5,9,13,17)] #remove empty columns ensg.ids=as.character(my.data[,1]) symbs=as.character(my.data[,2]) library(pathview) pathview(gene.data=ensg.ids, gene.idtype="ensembl", pathway.id="04060",species="hsa", out.suffix ="ensg") pathview(gene.data=symbs, gene.idtype="symbol", pathway.id="04060",species="hsa", out.suffix ="symb")
ADD COMMENTlink written 29 days ago by Luo Weijun1.4k
0
gravatar for Luo Weijun
29 days ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

if you have any unknown problem in R, you may also use the pathview web server:

https://pathview.uncc.edu/

ADD COMMENTlink written 29 days ago by Luo Weijun1.4k

Well I think I will have to do that : I try with your code and I still have the same bug. As well as my code, it works without the shinyApp, but once I give a try in teh app, nothing works, either with or without the app. I just hate my teacher for giving us that project right now ^^.

ADD REPLYlink written 28 days ago by Mataivic0

This seem to be a shiny problem instead of Pathview problem as the R code works well.

Sorry I can’t help more as I don’t use shiny.

ADD REPLYlink written 28 days ago by Luo Weijun1.4k
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