SnapATAC (version 1.0.0)

plotGene: Plot gene-body accessibility level

Description

Plot gene-body accessibility level

Usage

plotGene(obj, gene.names, viz.method, point.size, point.color, point.shape,
  background.point, background.point.color, background.point.alpha,
  background.point.size, background.point.shape, low.value, high.value,
  down.sample, seed.use, plot.nrow, plot.ncol, pdf.file.name, pdf.height,
  pdf.width, ...)

Arguments

obj

A snap object.

gene.names

Name of genes to plot.

viz.method

Visulization method c("tsne", "umap").

point.size

Point size [0.5].

point.color

Point color ["blue"].

point.shape

Point shape type [19].

background.point

If add points as background [TRUE].

background.point.color

Color of background points ["grey"].

background.point.alpha

Transparency level of background points [0.3].

background.point.size

Size of background points [0.5].

background.point.shape

Shape of background points [19].

low.value

Feature value is standarded to 0-1, value less than low.value will be set to low.value.

high.value

Feature value is standarded to 0-1, value greater than high.value will be set to high.value.

down.sample

Number of cells to plot. Cells will be randomly downsampled for this number for plotting.

seed.use

Random seed [10].

plot.nrow

Number of rows in the plot [3].

plot.ncol

Number of columns in the plot [3].

pdf.file.name

pdf file name to save the plot [NULL].

pdf.height

the height of the graphics region in inches [7].

pdf.width

the width of the graphics region in inches [7].

...

Arguments passed to plot method.

Examples

# NOT RUN {
data(demo.sp);
demo.sp = scaleCountMatrix(
obj=demo.sp,
mat="gmat",
cov=SnapATAC::rowSums(demo.sp, mat="bmat"),
method="RPM"
)
gene.names = c(
"Prdm14",   "E330040D14Rik", "Gm17971",       
"Gm17970",	"Defb44-ps",     "Gm7357",
"Gm37265",  "Kctd18",		"Gm37143"
)
plotGene(
obj=demo.sp, 
gene.names=gene.names, 
viz.method="tsne"
)
# }