degMDS {DEGreport} | R Documentation |
Uses cmdscale to get multidimensional scaling of data matrix, and plot the samples with ggplot2.
degMDS(counts, condition = NULL, k = 2, d = "euclidian", xi = 1, yi = 2)
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, c("euclidian", "cor"). |
xi |
number of component to plot in x-axis |
yi |
number of component to plot in y-axis |
ggplot2 object
data(humanGender) library(DESeq2) idx <- c(1:10, 75:85) dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx], colData(humanGender)[idx,], design=~group) degMDS(counts(dse), condition = colData(dse)[["group"]])