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 
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15 Euston Road, London, NW1 2BE. 



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