Plot one or more features by coloring cells in a UMAP plot.
Usage
plot_embedding(
source,
embedding,
features = NULL,
quantile_range = c(0.01, 0.99),
randomize_order = TRUE,
smooth = NULL,
smooth_rounds = 3,
gene_mapping = human_gene_mapping,
size = NULL,
rasterize = FALSE,
raster_pixels = 512,
legend_continuous = c("auto", "quantile", "value"),
labels_quantile_range = TRUE,
colors_continuous = c("lightgrey", "#4682B4"),
legend_discrete = TRUE,
labels_discrete = TRUE,
colors_discrete = discrete_palette("stallion"),
return_data = FALSE,
return_plot_list = FALSE,
apply_styling = TRUE
)Arguments
- source
Matrix, or data frame to pull features from, or a vector of feature values for a single feature. For a matrix, the features must be rows.
- embedding
A matrix of dimensions cells x 2 with embedding coordinates
- features
Character vector of features to plot if
sourceis not a vector.- quantile_range
(optional) Length 2 vector giving the quantiles to clip the minimum and maximum color scale values, as fractions between 0 and 1. NULL or NA values to skip clipping
- randomize_order
If TRUE, shuffle cells to prevent overplotting biases. Can pass an integer instead to specify a random seed to use.
- smooth
(optional) Sparse matrix of dimensions cells x cells with cell-cell distance weights for smoothing.
- smooth_rounds
Number of multiplication rounds to apply when smoothing.
- gene_mapping
An optional vector for gene name matching with match_gene_symbol(). Ignored if
sourceis a data frame.- size
Point size for plotting
- rasterize
Whether to rasterize the point drawing to speed up display in graphics programs.
- raster_pixels
Number of pixels to use when rasterizing. Can provide one number for square dimensions, or two numbers for width x height.
- legend_continuous
Whether to label continuous features by quantile or value. "auto" labels by quantile only when all features are continuous and
quantile_rangeis not NULL. Quantile labeling adds text annotation listing the range of displayed values.- labels_quantile_range
Whether to add a text label with the value range of each feature when the legend is set to quantile
- colors_continuous
Vector of colors to use for continuous color palette
- legend_discrete
Whether to show the legend for discrete (categorical) features.
- labels_discrete
Whether to add text labels at the center of each group for discrete (categorical) features.
- colors_discrete
Vector of colors to use for discrete (categorical) features.
- return_data
If true, return data from just before plotting rather than a plot.
- return_plot_list
If
TRUE, return multiple plots as a list, rather than a single plot combined using patchwork::wrap_plots()- apply_styling
If false, return a plot without pretty styling applied
