plotMDS: plotMDS

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

Generates a 2D MDS plot that can use the following inputs stored in an EMSet:

Usage

plotMDS(object, Dim1 = 1, Dim2 = 2, group = NULL, density = FALSE,
  PCA = TRUE)

Arguments

object	An EMSet.
Dim1	Dimension to plot on the x-axis.
Dim2	Dimension to plot on the y-axis.
group	(Optional) Name of the column in colInfo that describe a set of conditions you would like to colour cells by.
density	Vary alpha by density (Default: FALSE)
PCA	Use pre-calculated PCA-reduced values (Default: TRUE)

Details

1. Distance matrix generated by runCORE. 2. PCA matrix generated by runPCA. 3. Normalised, log-transformed count matrix stored in logcounts.

Value

A ggplot glob that contains a scatter plot.

Examples

# Load EMSet
em_set <- ascend::analyzed_set

# Generate MDS
mds_plot <- plotMDS(em_set, Dim1 = 1, Dim2 = 2, 
group = "cluster", PCA = TRUE)

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.