plotFeatureSingle: plotFeatureSingle

In r3fang/SnapATAC: Single Nucleus Analysis Package for ATAC-Seq

plotFeatureSingle

Description

plotFeatureSingle

Usage

plotFeatureSingle(obj, feature.value, method, point.size, point.shape,
  down.sample, pdf.file.name, pdf.width, pdf.height, quantiles, ...)

Arguments

obj	A snap object.
feature.value	Feature enrichment value for each cell. Value will be normalized betweeen 0 and 1.
method	Visulization method c("tsne", "umap").
point.size	Point size [1].
point.shape	Point shape type [19].
down.sample	Downsample the original cells to down.sample cells to ovoid large dataset [10,000].
pdf.file.name	pdf file name to save the plot [NULL].
pdf.width	Width of the graphics region in inches [7].
pdf.height	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.

Examples

data(demo.sp);
x = rexp(nrow(demo.sp));
x = (x-min(x))/(max(x)-min(x));
PlotFeatureSingle(
	obj=demo.sp, 
	feature.value=x,
	method="tsne", 
	point.size=1, 
	point.shape=19, 
	down.sample=10000, 
	pdf.file.name=NULL, 
	pdf.width=7, 
	pdf.height=7
)

r3fang/SnapATAC documentation built on March 29, 2022, 4:33 p.m.