tx_plot_metageneExons: Plot metagene exons

View source: R/tx_plots.R

tx_plot_metageneExonsR Documentation

Plot metagene exons

Description

Plot metagene exons

Usage

tx_plot_metageneExons(
  txDT,
  colVars,
  nBins,
  geneAnnot = NULL,
  nCores = 1,
  summ_fun = "mean",
  smooth = TRUE,
  spar = 0.5,
  plot_type = "lineplot",
  xLabelJump = 10,
  normalize = FALSE
)

Arguments

txDT

data.table. A table as output by the tx_makeDT_coverage(), tx_makeDT_nucFreq() or tx_makeDT_covNucFreq() functions.

colVars

character. Names of columns for which values will be extracted

nBins

integer. Number of bins into which exon data will be allocated.

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed().

nCores

integer. Number of cores to run the function with.

summ_fun

character. Summarizing function either "sum" or "mean". Default: "mean".

smooth

logical. Set to FALSE for not smoothing line.

spar

numeric. Smoothing parameter, typically (but not necessarily) in (0,1].

plot_type

character. Type of plot to be output, either "lineplot" or "boxplot".

xLabelJump

Number of bins to be skipped for label plotting

normalize

logical. If set to TRUE, values are normalized so that the area bellow the curve approximates to 1 for each variable.

Value

ggplot


AngelCampos/txtools documentation built on Sept. 16, 2024, 10:25 p.m.