DaMiR.MDSplot: Plot multidimentional scaling (MDS)

In DaMiRseq: Data Mining for RNA-seq data: normalization, feature selection and classification

Description

A MDS plot is drawn in order to visualize class clustering.

Usage

DaMiR.MDSplot(data, df, type = c("spearman", "pearson"))

Arguments

data	A SummarizedExperiment object or a matrix or a data.frame where rows and cols should be, respectively, observations and features
df	A data frame with class; it can be directly subset from data
type	A character string specifing the metric to be applied to correlation analysis. Either "spearman" or "pearson" is allowed; default is "spearman"

Details

The MDS plot is drawn taking as input a dissimilarity matrix produced by either a sample-per-sample Pearson's or Spearman's correlation of normalized expression data.

Value

A MDS plot, using only 'class' information

Author(s)

Mattia Chiesa, Luca Piacentini

Examples

# use example data:
data(data_reduced)
data(df)
# Draw MDS:
DaMiR.MDSplot(data=data_reduced, df=df, type="pearson")

DaMiRseq documentation built on Nov. 8, 2020, 5:53 p.m.