Simple R gists

Showcase short R examples

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License: GPL-3.0

National survey

- Deaths registered monthly in England and Wales

This notebook shows how to use readxl package to retreive the Deaths registered monthly in England and Wales Dataset from Office for National Statistics and create various plots to show the number of deaths with ggplot2.

- COVID-19 Vaccination Statistics in England

This notebook shows how to use readxl package to retreive the Monthly COVID-19 Vaccinations Dataset from NHS England and create various plots to show key statistics with ggplot2.

Gene expression

- Visualise differential expression analysis results with MA plot

This notebook shows readers how to use ggplot2 package to create various plots to show the magnitude of the change in expression between two groups (M) in comparison to the magnitude of average expression over all samples (A).

- Normalisation of bulk RNA-seq counts

This is a reproducible demo that shows readers how to use perform count normalisation of RNA-seq data using several common methods:

• DESeq2’s median-of-ratios
• edgeR’s TMM (trimmed mean of M-values)
• RPM/FPM/CPM (reads/fragments/counts per million mapped reads/fragments)
• TPM (transcripts per million mapped reads)
• RPKM/FPKM (reads/fragments per kilobase of transcript length per million mapped reads/fragments)

- Plot ligand-receptor expression on UMAP and t-SNE projection

This is a reproducible demo that shows readers how to use the function plotReducedDimLR which make use of the ggnewscale R package to ovelay the expressions of ligand and receptor genes on a single plot of UMAP or t-SNE projection.

Others

- Visualise interaction between 2 variables with parallel sets diagrams

This notebook shows readers how to use ggforce package to create parallel sets diagram to show the interaction between 2 categorical variables.

- Testing of the Spatial Image Analysis of Tissues (SPIAT) R package

This notebook shows how to use SPIAT to perform spatial data processing, quality control, visualization and analysis.