plotFeatureSingle.SnapATAC: plotFeatureSingle from SnapATAC package Allow the object can...

In beyondpie/pureRUtils: Commonly used R functions with pure R codes

plotFeatureSingle from SnapATAC package Allow the object can be a matrix of umap/tsne or a snap

Description

plotFeatureSingle from SnapATAC package Allow the object can be a matrix of umap/tsne or a snap

Usage

plotFeatureSingle.SnapATAC(
  snap = NULL,
  featureValue,
  embedmat = NULL,
  method = c("tsne", "umap"),
  pointSize = 0.1,
  pointShape = 19,
  downSample = 10000,
  pdfile = NULL,
  pdfWidth = 7,
  pdfHeight = 7,
  quantiles = c(0.01, 0.99),
  fontLab = 2,
  ...
)

Arguments

snap	A snap object, default is NULL
featureValue	Feature enrichment value for each cell. Value will be normalized betweeen 0 and 1.
embedmat	a matrix of umap or tsne, default is NULL
method	Visulization method c("tsne", "umap").
pointSize	Point size 1.
pointShape	Point shape type 19.
downSample	Downsample the original cells to down.sample cells to ovoid large dataset 10,000.
pdfile	pdf file name to save the plot NULL.
pdfWidth	Width of the graphics region in inches 7.
pdfHeight	Height of the graphics region in inches 7.
quantiles	Feature value outside this range will be removed c(0.01, 0.99)
...	Arguments passed to plot method.
fontLabl	integer default is 2

beyondpie/pureRUtils documentation built on Jan. 10, 2023, 3:22 a.m.