plotDEGRegression: plot the linear regression to show visualize the expression...

Description Usage Arguments Value

View source: R/plotDEAnalysis.R

Description

plot the linear regression to show visualize the expression the of DEGs identified by differential expression analysis

Usage

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plotDEGRegression(
  inSCE,
  useResult,
  threshP = FALSE,
  labelBy = NULL,
  nrow = 6,
  ncol = 6,
  defaultTheme = TRUE,
  isLogged = TRUE,
  check_sanity = TRUE
)

Arguments

inSCE

SingleCellExperiment inherited object. runMAST() has to be run in advance.

useResult

character. A string specifying the analysisName used when running a differential expression analysis function.

threshP

logical. Whether to plot threshold values from adaptive thresholding, instead of using the assay used by runMAST(). Default FALSE.

labelBy

A single character for a column of rowData(inSCE) as where to search for the labeling text. Default NULL.

nrow

Integer. Number of rows in the plot grid. Default 6.

ncol

Integer. Number of columns in the plot grid. Default 6.

defaultTheme

Logical scalar. Whether to use default SCTK theme in ggplot. Default TRUE.

isLogged

Logical scalar. Whether the assay used for the analysis is logged. If not, will do a log(assay + 1) transformation. Default TRUE.

check_sanity

Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE

Value

A ggplot object of linear regression


singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.