r2easyR.color: Assigns colors to reactivity values

In JPSieg/R2easyR: Facilitates Mapping Experimental RNA Reactivity Data to Secondary Structures Drawn with R2R

Assigns colors to reactivity values

Description

Assigns a color to each reactivity value in a dataframe. Also, saves a PDF legend and a PDF depicting the reactivity values in your current working directory.

Usage

r2easyR.color(
  data_frame,
  palette,
  no_data = "dimgrey",
  abs_reactivity_threshold = 0,
  manual.scale = FALSE,
  write_legend = TRUE
)

Arguments

data_frame	A data_frame containing reactivity values in a column labeled "Reactivity"
palette	A palette contisting of a vector containing 35 R colors. Compatible palettes are easily generated with r2easyR.palettes or r2easyR.custom.palette.
no_data	The color you want the nucleotide to have when there is no data. Default = "dimgrey"
abs_reactivity_threshold	Minimum threshold for reactivity data to be mapped to a color. Default = 0. Using a higher threshold prevents numerous, but low reactivity values from cluttering up the finished picture.
manual.scale	Manually specify a min and max. Useful if you want to color reactivity from multiple transcripts using 1 scale. Default is "FALSE". To set the scale, use manual.scale = c(min, max)
write_legend	Option to not write the legend or the Rxn plot. Default TRUE. If set to FALSE it will skip time consuming graphics writing steps. Good for running in bulk.

Value

A data frame containing a R2R label and Color column

JPSieg/R2easyR documentation built on March 2, 2024, 8:42 a.m.