SnapATAC (version 1.0.0)

plotFeatureSingle: 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

# NOT RUN {
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
)

# }