plot_ggheatmap: Plot a given position weight matrix as a heatmap using...

In snikumbh/archR: Identify Different Architectures of Sequence Elements

Description

The given matrix is plotted as a heatmap using ggplot2's geom_tile.

Usage

plot_ggheatmap(pwm_mat, pos_lab = NULL, pdf_name = NULL, fixed_coord = FALSE)

Arguments

pwm_mat	Matrix (usually a PWM, but can be non-normalized/any matrix) to be represented as a heatmap.
pos_lab	Labels for sequence positions, should be of same length as that of the sequences. Default value is NULL, when the positions are labeled from 1 to the length of the sequences.
pdf_name	Name of the file which will be saved as PDF.
fixed_coord	Set this to TRUE to use a fixed aspect ratio for the plot. Default is FALSE.

Value

A ggplot object so you can simply call print or save on it later. If pdf_name is given, it is also saved and the ggplot object returned.

See Also

plot_ggseqlogo for plotting PWMs as sequence logos

Other visualization functions: plot_ggseqlogo(), viz_bas_vec_heatmap_seqlogo(), viz_seqs_acgt_mat_from_seqs()

Examples

res <- readRDS(system.file("extdata", "example_archRresult.rds", 
         package = "archR", mustWork = TRUE))

pwm <- archR::make_dinuc_PWMs(get_clBasVec_m(res,iter=1)[,1], 
                        add_pseudo_counts = FALSE)

plot_ggheatmap(pwm_mat = pwm, fixed_coord = TRUE)

snikumbh/archR documentation built on July 5, 2021, 8:46 a.m.