degMDS: Plot MDS from normalized count data

Description Usage Arguments Value Examples

View source: R/clustering.R

Description

Uses cmdscale to get multidimensional scaling of data matrix, and plot the samples with ggplot2.

Usage

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degMDS(counts, condition = NULL, k = 2, d = "euclidian", xi = 1,
  yi = 2)

Arguments

counts

matrix samples in columns, features in rows

condition

vector define groups of samples in counts. It has to be same order than the count matrix for columns.

k

integer number of dimensions to get

d

type of distance to use

xi

number of component to plot in x-axis

yi

number of component to plot in y-axis

Value

ggplot2 object

Examples

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data(humanSexDEedgeR)
library(DESeq2)
idx <- c(1:10, 75:85)
dse <- DESeqDataSetFromMatrix(humanSexDEedgeR$counts[1:1000, idx],
humanSexDEedgeR$samples[idx,], design=~group)
degMDS(counts(dse), condition=colData(dse)$group)

Bioconductor-mirror/DEGreport documentation built on July 7, 2017, 10:53 p.m.