cellVisualization: visualize cells in 2D-dimensional space

Description Usage Arguments Value

View source: R/scAI_plotting.R

Description

visualize cells in 2D-dimensional space

Usage

1
2
3
4
cellVisualization(object, cell_coords, color.by, labels.order = NULL,
  colors.use = NULL, brewer.use = FALSE, xlabel = "UMAP1",
  ylabel = "UMAP2", title = NULL, label.size = 4, cell.size = 0.3,
  font.size = 10, do.label = F, show.legend = T, show.axes = T)

Arguments

object

scAI object

cell_coords

2D embedding coordinates of cells

color.by

the name of the variable in pData, defining cell groups, cells are colored based on the labels

labels.order

defining the factor level of cell groups

colors.use

defining the color for each cell group

brewer.use

use RColorBrewer palette instead of default ggplot2 color

xlabel

label of x-axis

ylabel

label of y-axis

title

main title of the plot

label.size

font size of the legend

cell.size

size of the dots

font.size

font size

do.label

label the cluster in 2D space

show.legend

whether show the legend

show.axes

whether show the axes

Value

ggplot2 object with 2D plot


sqjin/scAI documentation built on Nov. 19, 2020, 4:04 p.m.