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

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)