plotmics

Visualize omics and sequancing data in R

R package ggplot Omics

Adrià Mitjavila on June 23, 2021 Edited on October 05, 2021

Look at the source code here.

Look at the documentation here.

plOtMICS is an R package to visualize omics and sequencing data in R using simple but useful functions:

chromReads(): draws a ggplot2-based horizontal barplot with the number and the percentage of reads mapped to each chromosome.
barDEGs(): draws a ggplot2-based horizontal barplot with the upregulated and downregulated genes coming from DESeq2.
volcanoPlot(): draws a ggplot2-based volcano plot with the DE data coming out from DESeq2.
DEcompare(): draws a ggplot2-based scatter plot comparing the Log2FCs of two different contrasts.
barAnno(): takes a list of modified outputs from ChIPseeker::annotatePeak(), computes the proportion of peaks in distal or promoter regions and draws a ggplot2-based barplot with the correseponding proportion for each sample.
getVennCounts(): helper function that calls ChIPpeakAnno::makeVennDiagram() to intersect different sets of peaks and returns the Venn counts and a list of the peaks present in each set of peaks.
upsetPeaks(): calls getVennCounts() and draws an UpSet plot using the Venn counts and the UpSetR package.
ggUpsetPeaks(): calls getVennCounts() and draws a ggplot2-based UpSet plot using the Venn counts.
ggVennPeaks(): calls getVennCounts() and draws a Venn diagram using the package ggvenn.
plotDendogram(): helper function to draw a dendogram for the heatmaps in expressionHeatmap() and expressionHeatmap2().
expressionHeatmap(): function that takes a data frame of expression data (including Geneid) and plots a heatmap of the selected genes. It can be any expression data, but it is better for expression values, counts, normalized counts in which the frist column is the Geneid and the other columns are each of the samples that are to be plotted.
expressionHeatmap2(): function that takes a list of data frames with the columns Geneid and log2FoldChange (it can be another type data, such as FPKMs, but its easier to maintain the name of log2FoldChange since it is how it output from DESeq2) and plots a heatmap with the selected genes. It is better for log2FoldChange heatmaps in which each element in the list is a data frame that outputs from DESeq2.
chromRegions(): function that takes the chromosome size information and a list of regions (e.g. BED files) to draw the positions of that regions in the genome.
circleRegions(): function that takes a list of chromosome size information and a list of regions (e.g. BED files) to draw the positions of that regions in the genome. Similar to chromRegions(), but in a circular plot, allowing different assemblies, pairing regions, etc.

Install `plotmics`

To install plotmics, you have to run:

# install the devtools package from CRAN (only if you don't have it)
if(!require(devtools)){ install.packages("devtools"); library(devtools) }

# install plotmics from the GitHub repository
devtools::install_github("amitjavilaventura/plotmics")

If you want to use plotmics, go to the documentation to see how to run each function.

Versions

plotmics versions have the structure of 1.2.3. The first number (1, major) implies the addition of a function and/or major changes in the packages; the second number (2,minor) implies the addition of new features to a function and possible corrections; the third number (3, micro) implies the correction of minor bugs or addition of minor features.

The version history of plotmics is shown below:

v1.0.0:
- First version.

v1.1.0:
- Rescale ggVennPeaks() output to remove blank space around the Venn diagram.
- Add possibility to scale (scale()) data by rows or columns in expressionHeatmap() and expressionHeatmap2().

v1.1.1:
- Add minor formatting options in expressionHeatmap() and expressionHeatmap2(), such as the possibility to remove the gene names, change sizes of texts and titles, change the color of the border of each cell, etc.
- Add minor changes in ggVennPeaks() in order to make it easier to visualize more peaks sets.

v1.1.2:
- Change chromosome filtering method in chromReads().
- Allow dataframes without DEG column as input for volcanoPlot().
- Change scale = FALSE for scale = "none" in volcanoPlot().

v1.1.3:
- Fix error in labelling of expressionHeatmap() and expressionHeatmap2().

v1.1.4:
- Add possibility to color the NA values in expressionHeatmap() and expressionHeatmap2().
- Change title format in barDEGs().

v2.0.0 (2021-09-22):
- Add new function chromRegions().

v2.1.0 (2021-09-26):
- Allow chromRegions() to take a list of regions as input.
- Allow chromRegions() to order the region sets.

v3.0.0 (2021-09-28):
- Add new function circleRegions().
- Allow chromRegions() to color by different parameters.
- Allow chromRegions() to add extra info.
- Allow chromRegions() to remove or change size of text in the Y axis.

v3.0.1 (2021-09-30):
- Fix a minor bug about plotting the chromosome labels in circleRegions().
- Fix a minor bug in ggVennPeaks() that caused a intersection with one region more than expected.
- Remove pkgcond from required packages of getVennCounts().

v3.1.0 (2021-10-04):
- Allow ggVennPeaks() and getVennCounts() to consider strand information.

Contributors

This package has been developed by Adrià Mitjavila Ventura, with some contributions from dfernandezperez

If you want to contribute to this package, post an issue in this repository or fork it adding your code and do a pull request.

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