an ExpressionSet containing a matrix of expression values with rows representing features and columns samples
collapseDuplicateFeatures
logical, if TRUE multiple features per gene will be averaged
haveColDend
logical, if TRUE displays the grouping of samples using a dendrogram
Value
The result of the function is a plot.
Author(s)
Wolfgang Huber, 2013
See Also
myHeatmap2
Examples
data(x)
groups = with(pData(x), list(
"E3.25" = which(genotype=="WT" & Embryonic.day=="E3.25"),
"E3.5 (EPI)" = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="EPI"),
"E3.5 (PE)" = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="PE")))
samples = unlist(groups)
# heatmap of differentially expressed genes along the transition from E3.25 to E3.5
de = union(
getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (EPI)"),
getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (PE)"))
myHeatmap(x[de, samples], collapseDuplicateFeatures=TRUE)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(Hiiragi2013)
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
Loading required package: lattice
Attaching package: 'lattice'
The following object is masked from 'package:boot':
melanoma
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: XML
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: gtools
Attaching package: 'gtools'
The following objects are masked from 'package:boot':
inv.logit, logit
Loading required package: KEGGREST
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:AnnotationDbi':
select
The following object is masked from 'package:genefilter':
area
Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db
Loading required package: RColorBrewer
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Hiiragi2013/myHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: myHeatmap
> ### Title: Plot Heatmaps
> ### Aliases: myHeatmap
>
> ### ** Examples
>
> data(x)
> groups = with(pData(x), list(
+ "E3.25" = which(genotype=="WT" & Embryonic.day=="E3.25"),
+ "E3.5 (EPI)" = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="EPI"),
+ "E3.5 (PE)" = which(genotype=="WT" & Embryonic.day=="E3.5" & lineage=="PE")))
> samples = unlist(groups)
>
> # heatmap of differentially expressed genes along the transition from E3.25 to E3.5
> de = union(
+ getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (EPI)"),
+ getDifferentialExpressedGenes(x, groups, "E3.25", "E3.5 (PE)"))
> myHeatmap(x[de, samples], collapseDuplicateFeatures=TRUE)
>
>
>
>
>
> dev.off()
null device
1
>