plotCoverageData: Plot read coverage across a genomic region

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

Plot read coverage across a genomic region

Description

Does not work on Windows, because rtracklayer cannot read BigWig files on Windows.

Usage

plotCoverageData(
  coverage_data_list,
  heights = c(0.75, 0.25),
  alpha = 1,
  fill_palette = c("#a1dab4", "#41b6c4", "#225ea8"),
  connect_exons = TRUE,
  transcript_label = TRUE,
  return_subplots_list = FALSE,
  coverage_type = "area",
  show_legend = FALSE
)

Arguments

coverage_data_list	List of required from the extractCoverageData function: exons - list of GRanges objects, each object containing exons for one transcript. cdss - list of GRanges objects, each object containing the coding regions (CDS) of a single transcript. plotting_annotations - Transcript labels for plotting. tx_annotations - Transcript coordinates for plotting. xlabel - Label of the x-axis. coverage_df - Read coverage data frame. limits - x-axis limits.
heights	Specifies the proportion of the height that is dedicated to coverage plots (first value) relative to transcript annotations (second value). (default: c(0.75,0.25))
alpha	Transparency (alpha) value for the read coverage tracks. Useful to set to something < 1 when overlaying multiple tracks (see track_id). (default: 1)
fill_palette	Vector of fill colours used for the coverage tracks. Length must be equal to the number of unique values in track_data$colour_group column.
connect_exons	Print lines that connect exons together. Set to FALSE when plotting peaks (default: TRUE).
transcript_label	If TRUE then transcript labels are printed above each transcript. (default: TRUE).
return_subplots_list	Instead of a joint plot return a list of subplots that can be joined together manually.
coverage_type	Specifies if the read coverage is represented by either 'line', 'area' or 'both'. The 'both' option tends to give better results for wide regions. (default: area).
show_legend	display legend for the colour_group next to the read coverage plot (default: FALSE).

Value

Either object from cow_plot::plot_grid() function or a list of subplots (if return_subplots_list == TRUE)

Examples

require("dplyr")
require("GenomicRanges")
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)

selected_transcripts = c("ENST00000438495", "ENST00000392477") #Plot only two transcripts of the gens
## Not run: 
cov_data = extractCoverageData(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts], ncoa7_metadata, track_data)
plotCoverageData(cov_data, heights = c(2,1), fill_palette = getGenotypePalette())

## End(Not run)

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