Scatter plot for two-dimensional embeddings

Scatter plot for two-dimensional embeddings

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.

Author

Wei Liu

Note

nothing

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')