tx_plot_metageneRegions: Plot metagene by regions

View source: R/tx_plots.R

tx_plot_metageneRegionsR Documentation

Plot metagene by regions

Description

Plot metagene by regions

Usage

tx_plot_metageneRegions(
  txDT,
  geneAnnot,
  colVars,
  nBins_5UTR,
  nBins_CDS = NULL,
  nBins_3UTR = NULL,
  summ_fun = "mean",
  smooth = TRUE,
  spar = 0.5,
  nCores = 1,
  plot_type = "lineplot",
  normalize = FALSE
)

Arguments

txDT

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

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed().

colVars

character. Names of columns for which values will be extracted

nBins_5UTR

integer. Number of bins into which allocate data on 5'UTR regions

nBins_CDS

integer. Number of bins into which allocate data on CDS regions

nBins_3UTR

integer. Number of bins into which allocate data on 3'UTR regions

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].

nCores

integer. Number of cores to run the function with. Multicore capability not available in Windows OS. @param plot_type character. Type of plot to be output, either "lineplot" or "boxplot".

plot_type

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

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.