SnapATAC (version 1.0.0)

plotViz: 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

# NOT RUN {
data(demo.sp);
plotViz(
	obj=demo.sp, 
	method="tsne", 
	point.color="sample", 
	text.add=FALSE,
legend.add=TRUE
);

# }