plot_ccposition_den: Plot cell cycle position kernel density stratified by a...

In hansenlab/tricycle: tricycle: Transferable Representation and Inference of cell cycle

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
addRug	Whether to add rug on the bottom of the linear density plot or an inner circle on the circular plot to show the continuous scale of theta. Default: TRUE
RugPalette.v	The palette used for the rug plot. If not given, it will used the same default palette as in plot_emb_circle_scale.
...	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")

hansenlab/tricycle documentation built on March 19, 2022, 7:24 p.m.