plot: Visualization of a result of the DEXUS algorithm.

In dexus: DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

Description

Plots a heatmap of the log read counts of the top ranked genes or of selected genes.

Arguments

x	An instance of "CNVDetectionResult"
idx	The indices or the transcript names of the transcripts that should be visualized as heatmap.
cexSamples	Size of the column labels, i.e. the samples.
cexGenes	Size of the row labels, i.e. the transcripts.
newColNames	renames the samples.
type	Mark the samples, that do not belong to the major class by crosses ("crosses"), or boxes ("boxes").

Value

Generates a heatmap of the expression values of the top-ranked transcripts.

Author(s)

Guenter Klambauer [e-mail] and Thomas Unterthiner [e-mail]

Examples

data(dexus)
r <- dexus(countsBottomly[1:100, ])
plot(r)

Example output

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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'dexus'

The following object is masked from 'package:BiocGenerics':

    sizeFactors

Filtered out 5 % of the genes due to low counts
Unsupervised mode.

dexus documentation built on Nov. 8, 2020, 11:08 p.m.