NMFDoubletsPlotModuleThresholds: NMF Doublets: Plot module overlaps

In farrellja/URD: URD

Description

This plots each module pair (calculated by NMFDoubletsDefineModules) in terms of the proportion of 'overlapping' cells (on the x-axis) and the change in proportion of overlapping cells between the high and low thresholds (on the y-axis). This can be used to select parameters for choosing module pairs that likely identify doublets for use in NMFDoubletsDetermineCells. See documentation of NMFDoubletsDefineModules for more information.

Usage

NMFDoubletsPlotModuleThresholds(
  module.combos,
  frac.overlap.max,
  frac.overlap.diff.max,
  modules.highlight = NULL
)

Arguments

module.combos	(List) Output from NMFDoubletsDefineModules
frac.overlap.max	(Numeric) Value to highlight on x-axis as a potential parameter. (Maximum portion of cells that express both modules from a pair.)
frac.overlap.diff.max	(Numeric) Value to highlight on y-axis as a potential parameter. (Maximum change in proportion of cells that express both modules from a pair as the threshold is lowered.)
modules.highlight	(Character Vector) Any module pairs with both modules in this vector will be highlighted in green

Value

A ggplot2 object

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.