Visualization of TypoClust cell-type annotations

Visualizes cell-type annotation results generated by typoClust() using a composite layout combining label, tile, and dot plots.

Usage

typoClustVis(
  typoClust,
  desired_sets = NULL,
  rank_thresh = 1,
  refine = TRUE,
  refine_thresh = 1,
  order_by = c("Cell Type", "Cluster", "Combined Score", "Combined Count", "Purity"),
  title = NULL,
  subtitle = NULL,
  tag = NULL,
  cellType_palette = NULL,
  flip = FALSE,
  tile_width = 0.2,
  tile_height = 0.6,
  tile_xlim = c(0.5, 1.5),
  tile_legend_title = "Cell Type",
  dot_color_low = "blue",
  dot_color_high = "red",
  dot_panel_border_color = "black",
  dot_panel_border_size = 0.5,
  dot_axis_text_size = 11,
  dot_axis_title_size = 12,
  dot_plot_margin_right = 10,
  dot_xlab = "Lead Cell Type Score",
  dot_size_title = "Combined\nCount",
  dot_color_title = "Avg Purity",
  label_size = 3,
  label_padding_lines = 0.5,
  legend_box = "vertical",
  legend_box_just = "left",
  legend_position = "right"
)

Arguments

typoClust: An object of class TypoClust generated by typoClust().
desired_sets: Optional character vector specifying which clusters, sub-clusters, or cell subsets to visualize. If NULL, all sets in typoClust are shown.
rank_thresh: Integer specifying the top N ranked cell types to display per set.
refine: Logical; whether to refine annotations by traversing deeper into the cell-type hierarchy.
refine_thresh: Integer specifying how many hierarchical levels to traverse when refining cell types. Ignored if refine = FALSE.
order_by: Character string specifying how to order clusters in the plot. One of "Cell Type", "Cluster", "Combined Score", "Combined Count", or "Purity".
title: Optional character string specifying the plot title.
subtitle: Optional character string specifying the plot subtitle.
tag: Optional character string specifying a plot tag.
cellType_palette: A scale specification for coloring cell types. Can be either a ggplot2 scale object (e.g. ggplot2::scale_fill_hue()) or a character vector of colors.
flip: Logical; whether to flip plot axes.
tile_width: Numeric specifying tile width.
tile_height: Numeric specifying tile height.
tile_xlim: Numeric vector of length two specifying x-axis limits for tile plots.
tile_legend_title: Character string specifying the tile legend title.
dot_color_low: Character string specifying the low-end color of the dot color scale.
dot_color_high: Character string specifying the high-end color of the dot color scale.
dot_panel_border_color: Character string specifying the border color of dot panels.
dot_panel_border_size: Numeric specifying the border line width of dot panels.
dot_axis_text_size: Numeric specifying axis text size in the dot plot.
dot_axis_title_size: Numeric specifying axis title size in the dot plot.
dot_plot_margin_right: Numeric specifying the right margin of the dot plot.
dot_xlab: Character string specifying the x-axis label for the dot plot.
dot_size_title: Character string specifying the dot size legend title.
dot_color_title: Character string specifying the dot color legend title.
label_size: Numeric specifying label text size.
label_padding_lines: Numeric specifying vertical padding between labels.
legend_box: Character string specifying legend box orientation.
legend_box_just: Character string specifying legend box justification.
legend_position: Character string specifying legend position.

Value

A ggplot2 object representing the combined visualization.

Details

typoClustVis() displays the top-ranked cell types per cluster or cell subset, optionally refining annotations to deeper hierarchical levels. The visualization integrates categorical labels, quantitative annotation scores, marker support, and purity metrics.

Examples

if (FALSE) { # \dontrun{
p <- typoClustVis(
  typoClust = tc,
  rank_thresh = 1,
  refine = TRUE
)
print(p)
} # }