plot_dims: Plot a tSNE or umap colored by feature.

In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

Description

Plot a tSNE or umap colored by feature.

Usage

plot_dims(
  data,
  x = "UMAP_1",
  y = "UMAP_2",
  feature = NULL,
  legend_name = "",
  c_cols = pretty_palette2,
  d_cols = NULL,
  pt_size = 0.25,
  alpha_col = NULL,
  group_col = NULL,
  scale_limits = NULL,
  do_label = FALSE,
  do_legend = TRUE,
  do_repel = TRUE
)

Arguments

data	input data
x	x variable
y	y variable
feature	feature to color by
legend_name	legend name to display, defaults to no name
c_cols	character vector of colors to build color gradient for continuous values, defaults to pretty_palette
d_cols	character vector of colors for discrete values. defaults to RColorBrewer paired palette
pt_size	point size
alpha_col	whether to refer to data column for alpha values
group_col	group by another column instead of feature, useful for labels
scale_limits	defaults to min = 0, max = max(data$x), otherwise a two-element numeric vector indicating min and max to plot
do_label	whether to label each cluster at median center
do_legend	whether to draw legend
do_repel	whether to use ggrepel on labels

Value

ggplot object, cells projected by dr, colored by feature

Examples

plot_dims(
    pbmc_meta,
    feature = "classified"
)

clustifyr documentation built on Nov. 8, 2020, 5:32 p.m.