plot_emb_circle_scale: Plot embedding with cyclic cell cycle position

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

Plot embedding with cyclic cell cycle position

Description

Generate scat plot of embedding with cyclic cell cycle position or other cyclic variables

Usage

plot_emb_circle_scale(
  sce.o,
  color_by = "tricyclePosition",
  facet_by = NULL,
  dimred = 1,
  dim = seq_len(2),
  fig.title = NULL,
  point.size = 2.1,
  point.alpha = 0.6,
  x_lab = NULL,
  y_lab = NULL,
  hue.colors = c("#2E22EA", "#9E3DFB", "#F86BE2", "#FCCE7B", "#C4E416", "#4BBA0F",
    "#447D87", "#2C24E9"),
  hue.n = 500,
  plot.legend = FALSE
)

Arguments

sce.o	A SingleCellExperiment contains the embbing to be plotted against.
color_by	The name of variable in colData(sce.o) to be used to show colors. Default: "tricyclePosition"
facet_by	The name of variable in colData(sce.o) to be used to facet scatter plots. If used, the function will return a list of ggplot objects. If NULL, no faceted panels will be returned. Default: NULL
dimred	The name or index of reducedDims in SingleCellExperiment (reducedDims). Default: 1
dim	The indices of dimred to be plotted. At the moment, it has to be two integers. Default: 1:2
fig.title	The title of the figure. Default: NULL
point.size	The size of the point in scatter plot used by geom_scattermore. Default: 2.1
point.alpha	The alpha value (transparency) of the point in scatter plot used by geom_scattermore. Default: 0.6
x_lab	Title of x-axis. If not given, the colname of dimred will be used. Default: NULL
y_lab	Title of y-axis. If not given, the colname of dimred will be used. Default: NULL
hue.colors	The string vector gives the cyclic colors. The first color should look very similar to the last one. Default: c("#2E22EA", "#9E3DFB", "#F86BE2", "#FCCE7B", "#C4E416", "#4BBA0F", "#447D87", "#2C24E9")
hue.n	The number of breaks of color scheme. Default: 500
plot.legend	Whether the legend should be plotted with the scatter plot. We recommend not to use this legend but use the cyclic legend produced by circle_scale_legend instead. Default: FALSE

Details

This function help users plot embedding scater plot colored by cyclic variables, such as cell cycle position, which is bound between 0 - 2pi. It will take a SingleCellExperiment object as input, and plot out its dimred such as PCA, UMAP, and etc with a cyclic color scheme.

Value

A ggplot object or a list of ggplot objects. If facet_by is not assigned, a single ggplot plot of the scatter plot will be return, Otherwise, apart from the first scatter plot showing all cells together, other faceted scatter plots will also be given in the list.

Author(s)

Shijie C. Zheng

Examples

data(neurosphere_example, package = "tricycle")
neurosphere_example <- estimate_cycle_position(neurosphere_example)
plot_emb_circle_scale(neurosphere_example, point.size = 3.1, point.alpha = 0.8)

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