plot_dims: Scatter plot of cells in a two-dimensional embedding.

In hesselberthlab/scrunchy: Single Cell Reconstruction of Functional Heterogeneity

Description

This is the base plot for superimposing annotations like cell types, cluster assignments, and measured activities.

Usage

plot_dims(df, x, y, color = "cell_id", size = 0.1, alpha = 1,
  palette = "cloupe", labels = NULL, label_legend = TRUE,
  label_groups = FALSE)

Arguments

df	plot data
x	variable for x-axis
y	variable for y-axis
color	variable for point colors (default is black)
size	size for geom_point
alpha	alpha for geom_point
palette	palette for continuous colors. One of cloupe (the default), brewer, viridis.
labels	labels for groups
label_legend	add labels to legend
label_groups	add labels to points

Details

Embeddings can be calculated by calc_umap() and calc_tsne(), and retrieved with tidy_dims().

See Also

Other plot functions: plot_activity, plot_hairpin_coverage

Examples

plot_dims(fsce_tidy, UMAP1, UMAP2, size = 1)

plot_dims(fsce_tidy, UMAP1, UMAP2, IL7R, size = 1)

plot_dims(fsce_tidy, UMAP1, UMAP2, Uracil_45, size = 1)

plot_dims(fsce_tidy, UMAP1, UMAP2, k_cluster, size = 1)

plot_dims(fsce_tidy, UMAP1, UMAP2, k_cluster, labels = LETTERS[1:6])

plot_dims(fsce_tidy, UMAP1, UMAP2, k_cluster,
          labels = LETTERS[1:6], label_groups = TRUE)

hesselberthlab/scrunchy documentation built on Nov. 11, 2019, 2:29 p.m.