Plot metagene at CDS

Plot metagene at CDS

Usage

tx_plot_metageneAtCDS(
  txDT,
  geneAnnot,
  colVars,
  CDS_align,
  upFlank,
  doFlank,
  summ_fun = "mean",
  roll_fun = NULL,
  roll_n = 100,
  roll_align = "center",
  roll_fill = NA,
  smooth = TRUE,
  spar = 0.3,
  na.rm = TRUE,
  normalize = FALSE,
  tick_by = NULL
)

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

CDS_align

character. Either "start", "end", or "spliceSite" depending on the desired alignment, either to CDS start, CDS end, or splicing sites, respectively.

upFlank

numeric. Up-stream flank length

doFlank

numeric. Down-stream flank length

summ_fun

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

roll_fun

character. Rolling function either "sum" or "mean". Default: NULL

roll_n

numeric. Window size for rolling function

roll_align

character. Either "center" (default), "left" or "right"

roll_fill

vector. Either an empty vector (no fill), or a vector (recycled to) length 3 giving left, middle and right fills. NA by default

smooth

logical. Set to FALSE for not smoothing line.

spar

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

na.rm

logical. Omit all NAs from computations. Default: TRUE

normalize

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

tick_by

numeric. Distance between ticks in plot. Default: upFlank/2

Value

ggplot

See also

Smoothing function: smooth.spline().