genomic_regions_basic_stat: Visualize basic statistics on genomic regions

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Visualize basic statistics on genomic regions

Usage

genomic_regions_basic_stat(gr_list, subgroup = NULL, subgroup_color = NULL,
    title = paste0("Basic statistics for genomic regions"), species = "hg19",
    type = c("proportion", "number", "median_width"),
    chromosome = paste0("chr", c(1:22, "X", "Y")), by_chr = FALSE)

Arguments

gr_list	a list of GRanges.
subgroup	a vector which contains groups of samples. If it has names which correspond to gr_list, the order of this vector is automatically adjusted.
subgroup_color	colors corresponding to subgroups
title	title of the plot
species	species, necessary if type is set to proportion.
type	type of statistics
chromosome	subset of chromosomes
by_chr	take all chromosomes as a whole or calculate statistics for every chromosome

Details

The function makes barplot to visualize different statistics in all samples.

For type settings:

proportion

proportion of total length of regions in the whole genome.

number

number of regions. Sometimes only looking at the number of regions gives biased estimation of amount of regions if the width of regions are very viarable.

median_width

median width of regions

Value

A data frame which contains statistics for each chromosome in each sample.

Author(s)

Zuguang Gu <[e-mail]>

Examples

require(circlize)
set.seed(123)
gr_list = lapply(1:10, function(i) {
	df = generateRandomBed(1000)[1:sample(100:1000, 1), ]
	GRanges(df[[1]], ranges = IRanges(df[[2]], df[[3]]))
})
names(gr_list) = paste0("sample_", 1:10)
genomic_regions_basic_stat(gr_list)
genomic_regions_basic_stat(gr_list, subgroup = rep(letters[1:2], each = 5), 
    subgroup_color = c("a" = "red", "b" = "blue"))
genomic_regions_basic_stat(gr_list, subgroup = rep(letters[1:2], each = 5), 
    subgroup_color = c("a" = "red", "b" = "blue"), type = "number")
genomic_regions_basic_stat(gr_list, subgroup = rep(letters[1:2], each = 5), 
    subgroup_color = c("a" = "red", "b" = "blue"), type = "median_width")
genomic_regions_basic_stat(gr_list, subgroup = rep(letters[1:2], each = 5), 
    subgroup_color = c("a" = "red", "b" = "blue"), by_chr = TRUE)

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.