Description Usage Arguments Value
View source: R/RNAseq_plotting.R
Creates a MDS or PCA plot by passing GLimma::glMDSPlot output to ggplot2
1 2 3 4 5 6 7 8 9 10 11 | 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"
)
|
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 |
plot
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