plot_profile: Draw a profile plot

In PoisonAlien/peakseason: Functions for faster ChIP/ATAC-seq analysis and visualization.

Description

Draw a profile plot

Usage

plot_profile(mat_list, summarizeBy = "mean", color = NULL,
  ci = FALSE, legend_font_size = 1, condition = NULL,
  collapse_reps = TRUE, line_size = 2, axis_lwd = 3,
  axis_font_size = 1, sample_names = NULL, auto_y_axis = TRUE,
  y_lims = NULL)

Arguments

mat_list	Input matrix list generated by extract_matrix
summarizeBy	summarize matrix by mean or median. Default mean.
color	named vector of colors for each sample
ci	add SEM bars.
legend_font_size	cex for font size. Default 1.
condition	a column name in coldata containing sample conditions. Default NULL.
collapse_reps	Samples belonging to same condition to estimate average signal. Default TRUE if condition is given.
line_size	line width. Default 3.
axis_lwd	axis line width. Default 3.
axis_font_size	font size for axis. Default 1.
sample_names	names for samples. Default NULL parses from bigwig files.
auto_y_axis	Default TRUE. If FALSE plots from zero to max.
y_lims	Default NULL. Manually specify Y-limits.

Details

This function takes output from extract_matrix and draws a profile plot

PoisonAlien/peakseason documentation built on May 14, 2019, 4:01 a.m.