plotViz: Visulization

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

Visulization

Description

Visulization

Usage

plotViz(obj, method, point.size, point.shape, point.alpha, point.color,
  text.add, text.size, text.color, text.halo.add, text.halo.color,
  text.halo.width, legend.add, legend.pos, legend.text.size, legend.text.color,
  down.sample, pdf.file.name, pdf.width, pdf.height, ...)

Arguments

obj	A snap object.
method	Visulization method c("tsne", "umap").
point.size	Point size [1].
point.shape	Point shape type [19].
point.alpha	Point transparancy level [0.8].
point.color	Color of point. Two options, points color by cell cluster label or sample ID c("cluster", "sample").
text.add	Whether to add cluster label text at the centroid of each cluster [TRUE].
text.size	Cluster label text size [5].
text.color	Cluster label text color ["black"].
text.halo.add	Add halo to cluster label text [TRUE].
text.halo.color	Halo color ["white"].
text.halo.width	Halo width [0.5].
legend.add	Add a legend to the plot [FALSE].
legend.pos	Position of the legend c("bottomleft", "bottom", "left", "topleft", "top", "topright", "right", "center").
legend.text.size	Size of the text in the legend [1].
legend.text.color	Color of the text in the legend ["black"].
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	the width of the graphics region in inches [7].
pdf.height	the height of the graphics region in inches [7].
...	Arguments passed to plot method.

Examples

data(demo.sp);
plotViz(
	obj=demo.sp, 
	method="tsne", 
	point.color="sample", 
	text.add=FALSE,
legend.add=TRUE
);

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