plotScanpyMarkerGenesMatrixPlot: plotScanpyMarkerGenesMatrixPlot

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

plotScanpyMarkerGenesMatrixPlot

Description

plotScanpyMarkerGenesMatrixPlot

Usage

plotScanpyMarkerGenesMatrixPlot(
  inSCE,
  groups = NULL,
  nGenes = 10,
  groupBy,
  log2fcThreshold = NULL,
  parameters = "logfoldchanges",
  standardScale = "var",
  features = NULL,
  title = "",
  vmin = NULL,
  vmax = NULL,
  colorBarTitle = "log fold change"
)

Arguments

inSCE	Input SingleCellExperiment object.
groups	The groups for which to show the gene ranking. Default NULL means that all groups will be considered.
nGenes	Number of genes to show. Default 10
groupBy	The key of the observation grouping to consider. By default, the groupby is chosen from the rank genes groups parameter.
log2fcThreshold	Only output DEGs with the absolute values of log2FC larger than this value. Default NULL.
parameters	The options for marker genes results to plot are: ‘scores’, ‘logfoldchanges’, ‘pvals’, ‘pvals_adj’, ‘log10_pvals’, ‘log10_pvals_adj’. If NULL provided then it uses mean gene value to plot.
standardScale	Whether or not to standardize the given dimension between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Default NULL means that it doesn't perform any scaling.
features	Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes) to check their fold changes or p-values, instead of the top/bottom genes. The var_names could be a dictionary or a list. Default NULL
title	Provide title for the figure.
vmin	The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin. Default NULL
vmax	The value representing the upper limit of the color scale. Values larger than vmax are plotted with the same color as vmax. Default NULL
colorBarTitle	Title for the color bar.

Value

plot object

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- runScanpyNormalizeData(sce, useAssay = "counts")
sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
plotScanpyMarkerGenesMatrixPlot(sce, groupBy = 'Scanpy_louvain_1')

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.