create_mds_or_pca_plot: Creates a MDS or PCA plot by passing GLimma::glMDSPlot output...

Description Usage Arguments Value

View source: R/RNAseq_plotting.R

Description

Creates a MDS or PCA plot by passing GLimma::glMDSPlot output to ggplot2

Usage

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create_mds_or_pca_plot(
  loc_exp_lcpm,
  top = 500,
  dimensions = c(1, 2),
  gene.selection = "pairwise",
  factor_one = exp_DGElist$samples$treatment,
  factor_two = exp_DGElist$samples$RNAi,
  Title = "MDS plot using avg(logFC) as the distance",
  geom_size = 2.5,
  shape_legend_color = "grey"
)

Arguments

loc_exp_lcpm

Log transformed count matrix.

top

Top number of genes to be analysed e.g. top 500 genes

dimensions

PC dimensions to be plotted.

gene.selection

"pairwise" for MDS. "common" for PCA.

factor_one

Column of DGElist$samples that contains first factor to be labelled by color e.g. treatment

factor_two

Column of DGElist$samples that contains second factor to be labelled by shape e.g. RNAi

shape_legend_color

Value

plot


morriso1/tools4RNAseq documentation built on July 17, 2021, 3:07 a.m.