plotConsensus {MOCHA}

plotConsensus

Description

plotConsensus Extracts the peak reproducibility and generates a heuristic plots that can be used to determine the reproducibility threshold used within getSampleTileMatrix.

Usage

plotConsensus(
  tileObject,
  cellPopulations = "All",
  groupColumn = NULL,
  returnPlotList = FALSE,
  returnDFs = FALSE,
  numCores = 1
)

Arguments

tileObject

A MultiAssayExperiment object from callOpenTiles,

cellPopulations

the cell populations you want to visualize.

groupColumn

Optional parameter, same as in getSampleTileMatrix, which defines whether you want to plot reproducibility within each

returnPlotList

Instead of one plot with all celltypes/conditions, it returns a list of plots for each cell types

returnDFs

Instead of a plot, returns a data.frame of the reproducibility across samples. If set to false, then it plots the data.frame instead of returning it.

numCores

Number of cores to multithread over.

Value

SampleTileObj the input data structure with added gene annotations.