Question: KEGG2heatmap genesymbols as row names?
0
11.1 years ago by
Celine Carret220
Celine Carret220 wrote:
Dear BioC users, I want to plot the genes in my result-matrix that have an annotation in a given KEGG pathway as a heatmap. For that, I use the KEGG2heatmap function from the annotate package (see code below). I was wondering if anyone has an idea about how to change the default affy-IDs as row names in a KEGG2heatmap (or GO2heatmap) to have gene symbols or gene names for that matter displayed in the heatmap. Changing the probeset for gene symbols in the matrix doesn't work as the function uses the affy ID to query your matrix and find the probesets having the KEGG (or GO) annotation and put them in the heatmap output. I also tried to use labRow as in a normal heatmap but it doesn't work either. I then tried to write the object of the function and recover the order of the genes from the rowInd, thinking I could change this post-plot in a way, but this relates only to the number of genes found in there, so... not working! If anyone has an idea about how to solve this problem, I would be very grateful as I'm suppose to do many of those plots, and modifying them one after the other by adding the labRow=c("ICAM1","VCAM"...) accordingly for each GO or KEGG after checking for affy-ID to gene symbols is going to be long and painful. Thanks a lot and best wishes Celine NB: I know I didn't yet upgrade to the latest version of R and BioC, and I will, but in the meantime I would appreciate any suggestions to help me > library(affycoretools) > library(gplots) > library(mouse4302) > load("my.RData") > ls("package:mouse4302") > symbols1108_ids <- mget(rownames(matrix_eset_1108), envir=mouse4302SYMBOL) > matrix_eset_1108_symbols <- matrix_eset_1108 > rownames(matrix_eset_1108_symbols) <- symbols1108_ids > KEGG2heatmap("04514", matrix_eset_1108, data = "mouse4302", main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) ##gives what I expect, with row names written as probeset Affymetrix Ids > matrix_eset_1108_symbols <- cbind(symbols1108_ids,matrix_eset_1108) > KEGG2heatmap("04514", matrix_eset_1108_symbols, data = "mouse4302",main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) Error in heatmap(dataM, ...) : 'x' must be a numeric matrix > KEGG2heatmap("04514", matrix_eset_1108, data = "mouse4302",labRow=symbols1108_ids,main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) ## gives a heatmap with gene symbols as row names, however, the symbols do not correspond to the probeset ids, they do correspond to the ordering as in the rowInd: > CAMs <- KEGG2heatmap("04514", matrix_eset_1108, data = "mouse4302",main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) > names(CAMs) [1] "rowInd" "colInd" "Rowv" "Colv" > CAMs$rowInd [1] 9 11 6 7 8 1 5 10 2 12 4 3 ## those indexes relate to the order of the 12 genes found in the CAM pathway within my matrix, not across the whole matrix (1108 probesets). ## I identified this by running a KEGG2heatmap for a different pathway. The symbols were the same, only shuffled in a different order. > head(matrix_eset_1108_symbols) symbols1108_ids I_6hA I_6hB I_12hA I_12hB I_18hA I_18hB I_24hA I_24hB Non_6hA Non_6hB Non_12hA Non_12hB Non_18hA Non_18hB Non_24hA Non_24hB Psph "Psph" 9.527257 NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL Arfgef1 "Arfgef1" 11.25055 NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL Tbl3 "Tbl3" 8.922073 NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL Snapap "Snapap" 8.899586 NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL Cx3cl1 "Cx3cl1" 8.244229 NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL Gsn "Gsn" 7.061844 NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL > head(symbols1108_ids)$1415673_at [1] "Psph" $1415711_at [1] "Arfgef1"$1415750_at [1] "Tbl3" $1415756_a_at [1] "Snapap"$1415803_at [1] "Cx3cl1" $1415812_at [1] "Gsn" > head(matrix_eset_1108) I_6hA I_6hB I_12hA I_12hB I_18hA I_18hB I_24hA I_24hB Non_6hA Non_6hB Non_12hA Non_12hB Non_18hA Non_18hB 1415673_at 9.527257 9.838667 9.890481 10.020292 9.799559 9.904187 9.645748 9.445655 8.950675 8.943936 8.941548 8.823886 8.687042 9.178271 1415711_at 11.250548 11.217327 11.286776 11.223121 11.021241 11.113918 10.941252 10.794538 11.665688 11.510708 11.436264 11.455783 11.489206 11.264688 1415750_at 8.922073 8.952717 9.196360 9.139688 9.161736 9.141267 8.940151 8.859688 8.939075 8.748251 8.909915 9.044485 8.383893 8.578295 1415756_a_at 8.899586 8.894382 9.012984 9.148159 9.193082 8.982367 9.238500 9.427381 9.560140 9.428719 9.245954 9.178162 9.395412 9.180315 1415803_at 8.244229 7.768872 7.399605 7.107893 6.802274 6.212161 6.864431 6.767189 8.107881 7.942794 8.205100 8.188111 7.029770 7.136613 1415812_at 7.061844 7.754393 7.717294 7.922748 8.321420 8.339937 8.257631 8.064229 7.024239 7.139190 6.834602 7.163571 6.093165 6.861289 Non_24hA Non_24hB 1415673_at 9.129459 8.691872 1415711_at 11.490485 11.553578 1415750_at 8.495280 8.442697 1415756_a_at 9.230993 9.417729 1415803_at 7.105229 7.201890 1415812_at 6.961344 7.257823 > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 mouse4302_2.0.1 affycoretools_1.10.0 annaffy_1.10.0 KEGG_2.0.0 [8] GO_2.0.0 gcrma_2.10.0 matchprobes_1.10.0 biomaRt_1.12.0 RCurl_0.8-1 GOstats_2.4.0 Category_2.4.0 [15] genefilter_1.16.0 survival_2.32 RBGL_1.14.0 annotate_1.16.0 xtable_1.5-1 GO.db_2.0.0 AnnotationDbi_1.0.4 [22] RSQLite_0.6-3 DBI_0.2-3 graph_1.16.1 limma_2.12.0 affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.0 [29] Biobase_1.16.0 loaded via a namespace (and not attached): [1] cluster_1.11.9 XML_1.93-2 > ************************************** Celine Carret, PhD Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK tel.+44-1223494940 fax.+44-1223494919 ************************************** -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. [[alternative HTML version deleted]] annotation go annotate affy • 628 views ADD COMMENTlink modified 11.1 years ago by Saurin D. Jani360 • written 11.1 years ago by Celine Carret220 Answer: KEGG2heatmap genesymbols as row names? 0 11.1 years ago by Saurin D. Jani360 wrote: About Pathway to HEATMAP # Variable explanation: # esetSub2 = expression matirx # chiptype = annotation found from GeneChip, here 'hgu95a' # envPath2Probes = Environment # envGeneNames <- hgu95aGENENAME; # envPath2Probes <- hgu95aPATH2PROBE; # Generate Pathway Heatmap All_DE_Pathway <- aafPathway(geneNames(esetSub2), chiptype); unique(sapply(All_DE_Pathway, length)); pathlist <- do.call("c", All_DE_Pathway); pathL <- length(pathlist); pathmatrix <- sapply(pathlist, attributes); pathnamesX <- unique(t(pathmatrix)); kegg <- as.list(envPath2Probes); pathRow <- as.numeric(nrow(pathnamesX)); if(pathL >=1) { for(i in 1:pathRow) { pathID <- pathnamesX[,"id"][i]; pathID <- as.character(unlist(pathID)); pathName <- as.character(unlist(pathnamesX[,"name"][i])); pathName <- trimWhiteSpace(pathName); pathName <- sub("/", "_", pathName); pathName <- sub(" ", "_", pathName); pathName <- sub(" ", "_", pathName); pathName <- sub(" ", "_", pathName); pathName <- sub(" ", "_", pathName); pathName <- sub("-", "_", pathName); pathFile <- paste("Pathway",pathName,".jpeg",sep = "_"); pathSub <- paste(pathName,"Legend: Red = High, Blue = Low, White = Medium",sep = " "); pathSub <- paste("Date of Analysis:",date(),pathSub,sep = " "); Pathway2Heatmap(pathID,pathFile,pathSub); # check out the function below } } # if ends here # ########################################################### Pathway2Heatmap <- function(pathway,file,Hsub) { kegg <- as.list(envPath2Probes); pathProbes <- as.matrix(kegg[[pathway]]); # genes extracted from pathway esetSub2Genes <- as.matrix(geneNames(esetSub2)); temp <- as.matrix(rbind(unique(esetSub2Genes),unique(pathProbes))); temp1 <- as.matrix(temp[ as.matrix(duplicated(temp,))]); exp2 <- esetSub2[temp1]; exp2X <- exprs(exp2); pathDEGenes <- as.matrix(geneNames(exp2)); pathDEGeneNames <- mget(unique(pathDEGenes),env = envGeneNames,ifnotfound="No Annotation For this Probe"); row.names(exp2X) <- pathDEGeneNames; colnames(exp2X) <- samples; if (nrow(exp2X) > 1) { jpeg(filename= file,width=2000,height=2000); row.dist <- as.dist(1 - cor(t(exp2X))); Hsub <- c("Generated by EXAMPLE"); gmpalette <- bluered(64); heatmap.2(exp2X,col=gmpalette,Colv= FALSE,Rowv = as.dendrogram(hclust(row.dist,method="centroid")),scale="row",key=TRUE ,keysize=0.60,symkey=FALSE,density.info="none",trace="none",margins=c( 5,85),cexRow=1,cexCol=1, sub=Hsub,cex.sub=1); dev.off(which = dev.cur()); print("Pathway Heat map done"); }#if }#pathway2heatmap ########################################################### For more info. to run free web based analysis on your data http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage& process=Methods_Library_List Saurin -- |------------------------------------------------ | Saurin D. Jani | Bioinformatician | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29425 | | Email: jani at musc.edu | Phone: (843)792-1340 | Website: http://www.musc.edu/~jani |------------------------------------------------ Quoting Celine Carret <ckc at="" sanger.ac.uk="">: > Dear BioC users, > > > > I want to plot the genes in my result-matrix that have an annotation in > a given KEGG pathway as a heatmap. For that, I use the KEGG2heatmap > function from the annotate package (see code below). > > I was wondering if anyone has an idea about how to change the default > affy-IDs as row names in a KEGG2heatmap (or GO2heatmap) to have gene > symbols or gene names for that matter displayed in the heatmap. > > Changing the probeset for gene symbols in the matrix doesn't work as the > function uses the affy ID to query your matrix and find the probesets > having the KEGG (or GO) annotation and put them in the heatmap output. > > I also tried to use labRow as in a normal heatmap but it doesn't work > either. > > I then tried to write the object of the function and recover the order > of the genes from the rowInd, thinking I could change this post-plot in > a way, but this relates only to the number of genes found in there, > so... not working! > > If anyone has an idea about how to solve this problem, I would be very > grateful as I'm suppose to do many of those plots, and modifying them > one after the other by adding the labRow=c("ICAM1","VCAM"...) > accordingly for each GO or KEGG after checking for affy-ID to gene > symbols is going to be long and painful. > > > > Thanks a lot and best wishes > > Celine > > > > NB: I know I didn't yet upgrade to the latest version of R and BioC, and > I will, but in the meantime I would appreciate any suggestions to help > me > > > >> library(affycoretools) > >> library(gplots) > >> library(mouse4302) > >> load("my.RData") > >> ls("package:mouse4302") > >> symbols1108_ids <- mget(rownames(matrix_eset_1108), > envir=mouse4302SYMBOL) > >> matrix_eset_1108_symbols <- matrix_eset_1108 > >> rownames(matrix_eset_1108_symbols) <- symbols1108_ids > >> KEGG2heatmap("04514", matrix_eset_1108, data = "mouse4302", > main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), > col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) > > ##gives what I expect, with row names written as probeset Affymetrix Ids > > > >> matrix_eset_1108_symbols <- cbind(symbols1108_ids,matrix_eset_1108) > >> KEGG2heatmap("04514", matrix_eset_1108_symbols, data = > "mouse4302",main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), > col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) > > Error in heatmap(dataM, ...) : 'x' must be a numeric matrix > > > >> KEGG2heatmap("04514", matrix_eset_1108, data = > "mouse4302",labRow=symbols1108_ids,main="CAMs", > xlab="Samples",ylab="Genes",margins=c(9,9), > col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) > > ## gives a heatmap with gene symbols as row names, however, the symbols > do not correspond to the probeset ids, they do correspond to the > ordering as in the rowInd: > > > >> CAMs <- KEGG2heatmap("04514", matrix_eset_1108, data = > "mouse4302",main="CAMs", xlab="Samples",ylab="Genes",margins=c(9,9), > col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) > >> names(CAMs) > > [1] "rowInd" "colInd" "Rowv" "Colv" > >> CAMs$rowInd > > [1] 9 11 6 7 8 1 5 10 2 12 4 3 > > ## those indexes relate to the order of the 12 genes found in the CAM > pathway within my matrix, not across the whole matrix (1108 probesets). > > ## I identified this by running a KEGG2heatmap for a different pathway. > The symbols were the same, only shuffled in a different order. > > > >> head(matrix_eset_1108_symbols) > > symbols1108_ids I_6hA I_6hB I_12hA I_12hB I_18hA I_18hB > I_24hA I_24hB Non_6hA Non_6hB Non_12hA Non_12hB Non_18hA Non_18hB > Non_24hA Non_24hB > > Psph "Psph" 9.527257 NULL NULL NULL NULL NULL NULL > NULL NULL NULL NULL NULL NULL NULL NULL NULL > > > Arfgef1 "Arfgef1" 11.25055 NULL NULL NULL NULL NULL NULL > NULL NULL NULL NULL NULL NULL NULL NULL NULL > > > Tbl3 "Tbl3" 8.922073 NULL NULL NULL NULL NULL NULL > NULL NULL NULL NULL NULL NULL NULL NULL NULL > > > Snapap "Snapap" 8.899586 NULL NULL NULL NULL NULL NULL > NULL NULL NULL NULL NULL NULL NULL NULL NULL > > > Cx3cl1 "Cx3cl1" 8.244229 NULL NULL NULL NULL NULL NULL > NULL NULL NULL NULL NULL NULL NULL NULL NULL > > > Gsn "Gsn" 7.061844 NULL NULL NULL NULL NULL NULL > NULL NULL NULL NULL NULL NULL NULL NULL NULL > > >> head(symbols1108_ids) > > $1415673_at > > [1] "Psph" > > > >$1415711_at > > [1] "Arfgef1" > > > > $1415750_at > > [1] "Tbl3" > > > >$1415756_a_at > > [1] "Snapap" > > > > $1415803_at > > [1] "Cx3cl1" > > > >$1415812_at > > [1] "Gsn" > > > >> head(matrix_eset_1108) > > I_6hA I_6hB I_12hA I_12hB I_18hA I_18hB > I_24hA I_24hB Non_6hA Non_6hB Non_12hA Non_12hB Non_18hA > Non_18hB > > 1415673_at 9.527257 9.838667 9.890481 10.020292 9.799559 9.904187 > 9.645748 9.445655 8.950675 8.943936 8.941548 8.823886 8.687042 > 9.178271 > > 1415711_at 11.250548 11.217327 11.286776 11.223121 11.021241 11.113918 > 10.941252 10.794538 11.665688 11.510708 11.436264 11.455783 11.489206 > 11.264688 > > 1415750_at 8.922073 8.952717 9.196360 9.139688 9.161736 9.141267 > 8.940151 8.859688 8.939075 8.748251 8.909915 9.044485 8.383893 > 8.578295 > > 1415756_a_at 8.899586 8.894382 9.012984 9.148159 9.193082 8.982367 > 9.238500 9.427381 9.560140 9.428719 9.245954 9.178162 9.395412 > 9.180315 > > 1415803_at 8.244229 7.768872 7.399605 7.107893 6.802274 6.212161 > 6.864431 6.767189 8.107881 7.942794 8.205100 8.188111 7.029770 > 7.136613 > > 1415812_at 7.061844 7.754393 7.717294 7.922748 8.321420 8.339937 > 8.257631 8.064229 7.024239 7.139190 6.834602 7.163571 6.093165 > 6.861289 > > Non_24hA Non_24hB > > 1415673_at 9.129459 8.691872 > > 1415711_at 11.490485 11.553578 > > 1415750_at 8.495280 8.442697 > > 1415756_a_at 9.230993 9.417729 > > 1415803_at 7.105229 7.201890 > > 1415812_at 6.961344 7.257823 > > > > > >> sessionInfo() > > R version 2.6.0 (2007-10-03) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils datasets > methods base > > > > other attached packages: > > [1] gplots_2.3.2 gdata_2.3.1 gtools_2.4.0 > mouse4302_2.0.1 affycoretools_1.10.0 annaffy_1.10.0 > KEGG_2.0.0 > > [8] GO_2.0.0 gcrma_2.10.0 matchprobes_1.10.0 > biomaRt_1.12.0 RCurl_0.8-1 GOstats_2.4.0 > Category_2.4.0 > > [15] genefilter_1.16.0 survival_2.32 RBGL_1.14.0 > annotate_1.16.0 xtable_1.5-1 GO.db_2.0.0 > AnnotationDbi_1.0.4 > > [22] RSQLite_0.6-3 DBI_0.2-3 graph_1.16.1 > limma_2.12.0 affy_1.16.0 preprocessCore_1.0.0 > affyio_1.6.0 > > [29] Biobase_1.16.0 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.9 XML_1.93-2 > >> > > > > > > > > ************************************** > > Celine Carret, PhD > > Pathogen Microarrays > > Wellcome Trust Sanger Institute > > Hinxton, Cambridge > > CB10 1SA, UK > > tel.+44-1223494940 > > fax.+44-1223494919 > > ************************************** > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > > Limited, a charity registered in England with number 1021457 and a > compa > ny registered in England with number 2742969, whose registered > office is 2 > 15 Euston Road, London, NW1 2BE. > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >

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