Plot metagene exons — tx_plot_metageneExons • txtools

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