plotGene: Plot gene-body accessibility level

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

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

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"
)

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