jmw86069 / coverjam

Genome sequence coverage heatmaps around a central genome feature, such as transcript start site (TSS) or ChIP-seq/ATAC-seq peaks; or across a scaled genome region, such as gene locus regions from transcript start site (TSS) to transcript termination site (TTS).

coverjam

The goal of coverjam is to provide flexible methods to create genome sequence coverage heatmaps. These heatmaps typically represent sequence coverage (depth):

• around a central genome feature, such as transcript start site (TSS) or ChIP-seq/ATAC-seq peaks, or
• across a scaled genome region, such as the gene locus “body” defined from the transcript start site (TSS) to transcript termination site (TTS).

This package is mainly a wrapper around fantastic Bioconductor packages EnrichedHeatmap which extends ComplexHeatmap to render the heatmap.

The coverjam package provides additional methods:

• import coverage matrix data from multiple files
• define color gradients for each heatmap
• optionally handle coverage data in a group, which applies consistent numerical scales to the heatmap and corresponding meta-profile plot
• optionally apply row clustering by k-means or hierarchical clustering; offering correlation as an additional distance metric
• optionally split rows by aforementioned clustering, and/or by optional row annotations
• display row annotations alongside the heatmaps, in order to present additional context to the data displayed, for example chromosome, genome region type, additional metrics such as RNA-seq fold changes, etc.
• optionally apply numeric transformations (log2p1, sqrt, none)
• optionally sort rows by additional annotation, or by enriched signal using the EnrichedHeatmap metric.

Finally, coverjam intends to provide a re-usable command-line tool:

• apply an RMarkdown workflow to a set of coverage files, driven by
• configuration file used to customize the colors, numerical scales dimensions
• the method should be independent of user’s R environment, instead using the R environment of the installing user, setting the appropriate R_LIBS and RHOME variables to ensure the correct R is used.

Installation

You can install the development version of coverjam with:

# install.packages("remotes")
remotes::install_github("jmw86069/coverjam")

Notes

The methods are being migrated out of the platjam package, and into this package for more focused maintenance.