Creates a grid graphics plot of a dendrogram of Jensen-Shannon distances between conditions of a CuffFeatureSet or CuffGeneSet object.
Usage
## S4 method for signature 'CuffFeatureSet'
csDendro(object,logMode=T,pseudocount=1,replicates=FALSE)
## S4 method for signature 'CuffData'
csDendro(object,logMode=T,pseudocount=1,replicates=FALSE,...)
Arguments
object
An object of class 'CuffFeatureSet' or 'CuffGeneSet'
logMode
A logical argument to log10-transform FPKM values prior to plotting.
pseudocount
Value to be added to FPKM for appropriate log transformation and clustering. (Avoids zero-based errors)
replicates
A logical value whether or not to plot individual replicates or aggregate condition values.
...
Additional arguments to csHeatmap
Details
None
Value
Returns a dendrogram object and plots that object by default.
Note
None
Author(s)
Loyal A. Goff and Cole Trapnell
References
None.
Examples
data(sampleData)
csDendro(sampleGeneSet)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(cummeRbund)
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: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: 'fastcluster'
The following object is masked from 'package:stats':
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/csDendro.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csDendro
> ### Title: csDendro
> ### Aliases: csDendro csDendro,CuffFeatureSet-method
> ### csDendro,CuffData-method
> ### Keywords: heatmap
>
> ### ** Examples
>
> data(sampleData)
> csDendro(sampleGeneSet)
Using tracking_id, sample_name as id variables
'dendrogram' with 2 branches and 3 members total, at height 0.2482738
>
>
>
>
>
> dev.off()
null device
1
>