plot_ccposition_den {tricycle}R Documentation

Plot cell cycle position kernel density stratified by a factor

Description

The function will compute and plot cell cycle position kernel density.

Arguments

theta.v

The cell cycle position - a numeric vector with range between 0 to 2pi.

color_var.v

A factor variable to stratify theta.v, such as samples or 'CCStage'. The length of it should equal to the length of theta.v.

color_name

The name of the color_var.v to be used in the legend.

palette.v

A string vector to give the color names. It should has the length of the number of levels of color_var.v. If not given, the 'Set1' palette will be used. (See display.brewer.all) If the number of levels of color_var.v is greater than 8, only the top 8 levels of most cell will be shown. You can show them all by feeding enough colors in palette.v. Default: NULL

fig.title

The title of the figure. Default: NULL

type

It can be either of 'linear' or 'circular'. 'linear' corresponds to Cartesian coordinate system and 'circular' for polar coordinate system. Default: 'linear'

bw

The smoothing bandwidth to be used. It is equal to the concentration parameter of the von Mises distribution. See density.circular. Default: 30

weighted

Whether the density should be weighted on the percentage of each level of color_var.v. Default: FALSE

line.size

The size of the line used by geom_path. Default: 0.5

line.alpha

The alpha value of the line used by geom_path. Default: 0.5

...

Other arguments accepted by geom_path.

Details

The function first estimates kernel density using the von Mises distribution. Then, it plots out the density in the polar coordinate system or Cartesian coordinate system. Different colors represents different levels of color_var.v and the dashed black line is the marginal distribution of all cells.

Value

A ggplot object

Author(s)

Shijie C. Zheng

See Also

estimate_Schwabe_stage, for inferring 5 stages of cell cycle

Examples

data(neurosphere_example, package = "tricycle")
neurosphere_example <- estimate_cycle_position(neurosphere_example)
plot_ccposition_den(neurosphere_example$tricyclePosition, neurosphere_example$sample, "sample")

neurosphere_example <- estimate_Schwabe_stage(neurosphere_example,
 gname.type = "ENSEMBL", species = "mouse")
plot_ccposition_den(neurosphere_example$tricyclePosition, neurosphere_example$CCStage, "CCStage")

[Package tricycle version 1.1.1 Index]