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Question: Pathview question
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gravatar for Luo Weijun
4.6 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Demitry, In pathview function, please look into the argument gene.idtype. Default gene.idtype="entrez",i.e. Entrez Gene, which are the primary KEGG gene ID for many common model organisms. For other species, gene.idtype should be set to "KEGG" as KEGG use other types of gene IDs. For more details check the help info: ?pathview HTH, Weijun -------------------------------------------- On Wed, 4/23/14, Dmitry wrote: Subject: Re: Pathview question Date: Wednesday, April 23, 2014, 3:38 PM Hi?Weijun, Thanks, this was dumb error. My biocLite was out of date so even though I downloaded pathview recently I was still getting old versions. I found the bug in version 1.1.4, but using the newer version everything also works. I have one question, why do you not accept the native IDs that KEGG uses for some organisms. My specific example is for Arabidopsis. KEGG uses TAIR ids, and this is what pathview also returns as kegg.names. But to get the genes to map I have to convert TAIR to entrez which is then converted back to TAIR. [[elided Yahoo spam]] -Dmitry On Wed, Apr 23, 2014 at wrote: Dmitry, Thanks for your interest. you are working with the old pathview_1.1.4. the package has been updated multiple times. any version >=1.1.5 would work with you data. To make full use of all functions, I would suggest you to install the latest release version 1.4.0: http://bioconductor.org/packages/release/bioc/html/pathview.html Note that you don?t have to upgrade R or Bioconductor, just manually download the package for your OS (windows here): install.packages("/your/local/directory/pathview_1.4.0.zip", repos = NULL) or you may try r-forge: install.packages("pathview",repos="http://R-Forge.R-project.org") HTH, Weijun -------------------------------------------- On Tue, 4/22/14, Dmitry wrote: ?Subject: Pathview question ?Date: Tuesday, April 22, 2014, 2:39 PM ?Dear?Weijun, ?Thank you for your excellent work on the R ?package pathview. It is a very impressive an useful tool. ?I've had good success reproducing all the tutorial ?examples, but am running into issues using my own data and ?am wondering if you could point to my problem? ?Here is example code to generate a network for ?Arabidopsis. I can map compounds just fine, but not ?genes.? ?I've specifically selected all the genes for ?the pathway for my tests. Using Entrez IDs as input no genes ?are recognized. Using the native KEGG IDs all genes are ?recognized but all the color mappings are set to =0. ?#-----------------------------------------------------library(pathvi ew) ?#gene data as ENTREZ ?IDsgene.data.entrez<-structure(list(comp1 ?= c(-1.33993867494585, -0.874075185878206,? ?-0.815437861373184, 1.99784067931179, ?-1.80615547306295, ?2.87929513486298,?3.19461607237897, ?0.156449901575116, -2.57802582052787, ?1.68618727880872,?-2.23921303962625, ?1.60273066264584, 3.29143350796589, ?0.674562473202573,? ?0.942955331710717)), .Names = "comp1", ?row.names = ?c("824798",?"816781", ?"837777", "828186", "823737", ?"841200", "843630", ?"838927",? ?"837834", "821313", ?"831938", "842023", "824610", ?"819837", "821171"), class = ?"data.frame") ?pv.out <- pathview(gene.data = ?gene.data.entrez,pathway.id = ?"00052", species = "ath", out.suffix = ?"test",keys.align = "y", ?kegg.native = T, match.data=F, key.pos = ?"topright") ?pv.out ?and image ?#Using native KEGG ?Ids?gene.data<-structure(list(comp1 = ?c(-1.33993867494585, ?-0.874075185878206,?-0.815437861373184, ?1.99784067931179, -1.80615547306295, ?2.87929513486298,? ?3.19461607237897, 0.156449901575116, -2.57802582052787, ?1.68618727880872,?-2.23921303962625, ?1.60273066264584, 3.29143350796589, ?0.674562473202573,?0.942955331710717)), .Names = ?"comp1", row.names = ?c("AT3G56310",? ?"AT2G22480", "AT1G12240", ?"AT4G01970", "AT3G45940", ?"AT1G47840",?"AT1G72990", ?"AT1G23190", "AT1G12780", ?"AT3G03250", "AT5G18200",? ?"AT1G55740", "AT3G54440", ?"AT3G06580", "AT3G01260"), class = ?"data.frame") ?pv.out <- pathview(gene.data = ?gene.data, ?pathway.id = "00052", ?species = "ath", out.suffix = ?"test",keys.align = "y", ?kegg.native = T, match.data=F, key.pos = ?"topright") ?pv.out ?# and the image ?#Now all the genes are recognized but set to ?zero?#-------------------------------------------------------------- ------- ?Thank you in advance for any ?guidance. ?Best,Dmitry ?sessionInfo()R version 3.0.1 ?(2013-05-16) ?Platform: i386-w64-mingw32/i386 (32-bit) ?locale:[1] LC_COLLATE=English_United ?States.1252 ?LC_CTYPE=English_United States.1252 ? ??LC_MONETARY=English_United States.1252[4] ?LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? ?LC_TIME=English_United States.1252 ? ? ?attached base packages:?[1] splines ?? grid ? ? ?compiler ?parallel ?stats ? ? graphics ??grDevices utils ? ? datasets ?methods ? base ? ??? ?other attached packages: ??[1] CTSgetR_1.0 ? ? ? ? ? ? ? ??org.At.tair.db_2.9.0 ? ? ? iplots_1.1-6 ? ? ? ? ? ?? ? rJava_0.9-4 ? ? ? ? ? ? ? ?FSelector_0.19 ? ?? ? ? ? ??[6] qvalue_1.34.0 ? ? ? ? ? ?? ?fastICA_1.1-16 ? ? ? ? ? ? ClassComparison_2.15.1 ?? ? PreProcess_2.12.3 ? ? ? ? ?oompaBase_3.0.0 ? ? ?? ? ?? ?[11] IDPmisc_1.1.17 ? ? ? ? ? ? lattice_0.20-15 ?? ? ? ? ? ?ICSNP_1.0-9 ? ? ? ? ? ? ? ??ICS_1.2-3 ? ? ? ? ? ? ? ? ?survey_3.29-4 ? ? ? ?? ? ??[16] mvtnorm_0.9-9994 ? ? ? ? ? ?aroma.light_1.30.0 ? ? ? ? matrixStats_0.6.2 ? ? ? ? ??PerformanceAnalytics_1.1.0 xts_0.9-3 ? ? ? ? ? ? ? ??? ?[21] zoo_1.7-9 ? ? ? ? ? ? ? ? ??splancs_2.01-32 ? ? ? ? ? ?sp_1.0-8 ? ? ? ? ? ?? ? ? ? ellipse_0.3-7 ? ? ? ? ? ? ?geometry_0.3-2 ?? ? ? ? ? ?[26] magic_1.5-4 ? ? ? ? ? ?? ? ?abind_1.4-0 ? ? ? ? ? ? ? ?rgl_0.93.928 ? ?? ? ? ? ? ? ROCR_1.0-4 ? ? ? ? ? ? ? ? ?car_2.0-16 ? ? ? ? ? ? ? ? ?[31] nnet_7.3-6 ? ? ? ? ? ? ? ? pls_2.3-0 ? ? ?? ? ? ? ? ? ?nortest_1.0-2 ? ? ? ? ? ? ??pcaMethods_1.50.0 ? ? ? ? ?Rcpp_0.10.3 ? ? ? ? ? ?? ??[36] pvclust_1.2-2 ? ? ? ? ? ? ??psych_1.3.2 ? ? ? ? ? ? ? ?pheatmap_0.7.4 ? ? ? ?? ? ? gplots_2.11.0.1 ? ? ? ? ? ?MASS_7.3-26 ? ? ?? ? ? ? ?? ?[41] KernSmooth_2.23-10 ? ? ? ? caTools_1.14 ? ? ?? ? ? ? ? gdata_2.12.0.1 ? ? ? ? ? ? gtools_2.7.1 ?? ? ? ? ? ? ? outliers_0.14 ? ? ? ? ? ???[46] pathview_1.1.4 ? ? ? ? ? ? ?org.Hs.eg.db_2.9.0 ? ? ? ? RSQLite_0.11.3 ? ? ? ? ? ?? DBI_0.2-7 ? ? ? ? ? ? ? ? ?AnnotationDbi_1.22.5 ?? ? ? ?[51] Biobase_2.20.0 ? ? ? ? ? ? ?BiocGenerics_0.6.0 ? ? ? ? BiocInstaller_1.10.4 ? ? ? ?KEGGgraph_1.16.0 ? ? ? ? ? graph_1.38.0 ? ? ? ? ? ?? ?[56] XML_3.96-1.1 ? ? ? ? ? ? ? ?KEGGREST_1.0.1 ? ? ? ? ? ? linkcomm_1.0-8 ? ? ? ? ?? ? RColorBrewer_1.0-5 ? ? ? ? igraph_0.6.5-1 ? ? ? ?? ? ? ?[61] rcom_2.2-5 ? ? ? ? ? ? ? ? rscproxy_2.0-5 ?? ? ? ? ? ? RCurl_1.95-4.1 ? ? ? ? ? ? ?bitops_1.0-5 ? ? ? ? ? ? ? ?loaded via a namespace (and not ?attached):?[1] Biostrings_2.28.0 ? digest_0.6.3 ?? ? ? ?dynamicTreeCut_1.21 httr_0.2 ? ? ? ? ? ??IRanges_1.18.0 ? ? ?png_0.1-6 ? ? ? ? ? ?R.methodsS3_1.4.2 ? ??[8] randomForest_4.6-7 ?Rgraphviz_2.4.0 ? ? ?RJSONIO_1.0-3 ? ? ? RWeka_0.4-17 ? ? ? ??RWekajars_3.7.9-1 ? stats4_3.0.1 ? ? ? ?stringr_0.6.2 ?? ? ?[15] tcltk_3.0.1 ? ? ? ? tools_3.0.1 ?? ? ? ?>?
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