PlotContributionStructure: Plot contribution structure (diversity) of the complexes (a...

In mahfuz05062/FLEX_R: FunctionaL Evaluation of eXperimental perturbation (i.e. genome wide knockout) screens

Description

Plot contribution structure (diversity) of the complexes (a muller plot)

Usage

PlotContributionStructure(
  plot.data,
  cutoff.all = NULL,
  min.pairs = 10,
  min.precision.cutoff = 0.5,
  num.complex.to.show = 10,
  show.legend = TRUE,
  list.of.complexes.to.show = NULL,
  alternative.names = NULL,
  ccol = NULL,
  y.lim = NULL,
  fig.title = NULL,
  fig.labs = c("Fraction of TP", "Precision"),
  outfile.name = "test_cont_str",
  outfile.type = "pdf",
  save.figure = FALSE
)

Arguments

plot.data	a complex (unique) vs precision matrix where each element denote number of TP at that combination
cutoff.all	all the precision cutoffs used here (the same as used for plot.data)
min.pairs	all the precision cutoffs used here (the same as used for plot.data)
min.precision.cutoff	How far down should we go in precision cutoff to calcualte contribution of complexes? Default is 0.5, meaning we calculate contributions starting from the highest precision (where we have at least min.pairs) to the min.precision.cutoff and take a mean contribution to rank the complexes.
num.complex.to.show	How many complexes we want to show (everything else will be put to others)?
show.legend	default TRUE. Set to FALSE if we don't want to print legends.
list.of.complexes.to.show	Use this list of complex to show on the plot, regardless of their ranking.
alternative.names	Provide a list of names (corresponds to list.of.complexes.to.show) to use as alternative to original names
ccol	colors for the top complexes highlighted (top 10 contributing complexes are colored by default)
fig.title	title in case we want to save the image
fig.labs	x and y axis labels
outfile.name	name of the output file
outfile.type	type of figure to save - 'pdf' (default) or 'png'
save.figure	do we want to save or just plot

mahfuz05062/FLEX_R documentation built on May 27, 2021, 4:32 a.m.