plot_scatter: Scatter plot for two-dimensional embeddings

In PRECAST: Embedding and Clustering with Alignment for Spatial Datasets

Scatter plot for two-dimensional embeddings

Description

Scatter plot for two-dimensional embeddings

Usage

  plot_scatter(embed_use, meta_data, label_name, 
    xy_names=c('tSNE1', 'tSNE2'), no_guides = FALSE, 
    cols = NULL, 
    point_size = 0.5, point_alpha=1, 
    base_size = 12, do_points = TRUE, do_density = FALSE, border_col='gray',
    legend_pos='right', legend_dir='vertical', nrow.legend=NULL)

Arguments

embed_use	an object named "Seurat", "maxtrix" or "dgCMatrix". The object of class "Seurat" must include slot "scale.data".
meta_data	an optional positive integer, specify the number of features to be extracted.
label_name	the size of point in the scatter plot.
xy_names	the text size in the plot.
no_guides	whether display the legend.
cols	colors used in the plot.
point_size	the point size of scatter plot.
point_alpha	the transparency of the plot.
base_size	the base text size.
do_points	Plot point plot.
do_density	Plot density plot
border_col	the border color in the plot.
legend_pos	the position of legend.
legend_dir	the direction of legend.
nrow.legend	the number of rows of legend.

Details

Nothing

Value

Return a ggplot2 object.

Note

nothing

Author(s)

Wei Liu

See Also

None

Examples

  embed_use <- cbind(1:100, sin((1:100)*pi/2))
  meta_data <- data.frame(cluster=factor(rep(1:2, each=50)))
  plot_scatter(embed_use, meta_data, label_name='cluster')

PRECAST documentation built on May 29, 2024, 3 a.m.