plotCoverageFromUCSC: Plot read coverage directly from UCSC OrgDb and TxDb objects.

In kauralasoo/wiggleplotr: Make read coverage plots from BigWig files

Plot read coverage directly from UCSC OrgDb and TxDb objects.

Description

A wrapper around the plotCoverage function. See the documentation for (plotCoverage) for more information.

Usage

plotCoverageFromUCSC(orgdb, txdb, gene_names, transcript_ids = NULL, ...)

Arguments

orgdb	UCSC OrgDb object.
txdb	UCSC TxDb obejct.
gene_names	List of gene names to be plotted.
transcript_ids	Optional list of transcript ids to be plotted.
...	Additional parameters to be passed to plotCoverage.

Value

ggplot2 object

Examples

require("dplyr")
require("GenomicRanges")
require("org.Hs.eg.db")
require("TxDb.Hsapiens.UCSC.hg38.knownGene")

orgdb = org.Hs.eg.db
txdb = TxDb.Hsapiens.UCSC.hg38.knownGene

sample_data = dplyr::data_frame(sample_id = c("aipt_A", "aipt_C", "bima_A", "bima_C"), 
 condition = factor(c("Naive", "LPS", "Naive", "LPS"), levels = c("Naive", "LPS")), 
 scaling_factor = 1) %>%
 dplyr::mutate(bigWig = system.file("extdata",  paste0(sample_id, ".str2.bw"), package = "wiggleplotr"))
 
track_data = dplyr::mutate(sample_data, track_id = condition, colour_group = condition)
## Not run: 
#Note: This example does not work, becasue UCSC and Ensembl use different chromosome names
plotCoverageFromUCSC(orgdb, txdb, "NCOA7", transcript_ids = c("ENST00000438495.6", "ENST00000368357.7"), 
track_data, heights = c(2,1), fill_palette = getGenotypePalette())

## End(Not run)

kauralasoo/wiggleplotr documentation built on July 4, 2022, 11:43 a.m.