plot_dots: Plot dots

In Terkild/scutility: Utility Functions For Multi-modal Single-cell Analysis

Plot dots

Description

Plots population/cluster statistics as percentage positive (dot size) and mean expression within positive population (color)

Usage

plot_dots(
  sce,
  rows = SingleCellExperiment::colLabels(sce),
  rows_colors = NA,
  rows_colors_width = 0.02,
  rows_distribution_by = NA,
  rows_distribution_fill = NULL,
  rows_distribution_width = 0.05,
  colnames_fun = function(x) {
     return(as.factor(x))
 },
  coldata = SingleCellExperiment::colData(sce),
  assay_color = "logcounts",
  assay_positive = "fg_prob",
  threshold_positive = 0.95,
  threshold_color = 2,
  threshold_fraction = 0.05,
  feature_annotation = NULL,
  feature_annotation_height = 0.1,
  max.cutoff = NA,
  gaps_y = NA,
  scale_fill = scale_fill_viridis_c(option = "turbo")
)

Arguments

sce	SingleCellExperiment object containing expression matrices
rows	colData column defining clustering to be used as rows
rows_colors	rows can be color annotated by providing a named color palette here
rows_colors_width	Relative (to 1) width of rows color annotation
rows_distribution_by	Plot how cluster is distributed among another colData column
rows_distribution_fill	Colors palette (color vector) for cluster distribution
rows_distribution_width	Relative (to 1) width of rows distribution plot
colnames_fun	Function to clean up rownames (such as trimming prefix)
coldata	DataFrame containing cluster information for each column in the provided matrices. Defaults to colData(sce)
assay_color	Name of SCE assay to use for coloring dots
assay_positive	Name of SCE assay to use for gating positive cells
threshold_positive	Threshold for gating positive cells
threshold_color	Only positive populations having a mean expression above this threshold will be displayed
threshold_fraction	Minimum fraction of cells to be included in the plot
feature_annotation	Annotation data.frame for features (columns) to be shown as a heatmap
feature_annotation_height	Relative (to 1) height of feature annotation heatmap
max.cutoff	Cutoff value for upper limit (can be integer or 'q' value for quantile: 'q95' sets at 95% percentile)
gaps_y	Not currently used
scale_fill	ggplot scale_fill_continuous function for coloring dots

Value

ggplot2 combined with patchwork

Terkild/scutility documentation built on Jan. 16, 2025, 5:28 p.m.