Visualize cluster and cell-subset markers — markoClustVis • celliverse

Generates a faceted dot plot for visualizing marker genes across clusters, sub-clusters, or cell subsets stored in a ClustoCell or MarkoCell object. Marker selection can be controlled by rank or by selecting the top n markers per group. Dot size and color can represent marker purity or marker class.

Usage

markoClustVis(
  obj,
  desired_sets = NULL,
  show_pos_markers = TRUE,
  show_neg_markers = FALSE,
  show_med_markers = FALSE,
  thresh_mode = c("n", "rank"),
  thresh = 5,
  title = NULL,
  subtitle = NULL,
  tag = NULL,
  nrow_panels = NULL,
  dotsize = 2,
  show_purity = TRUE,
  class_palette = NULL,
  color_low = "blue",
  color_high = "red",
  panel_border_color = "black",
  panel_border_size = 0.5,
  axis_text_size = 7,
  axis_title_size = 8,
  plot_margin_right = 10,
  xlab = "Rank",
  ylab = "Marker",
  show_legend = TRUE,
  legend_box = "vertical",
  legend_box_just = "left",
  legend_position = "right"
)

Arguments

obj

An object of class ClustoCell or MarkoCell containing marker information.

desired_sets

Optional character vector specifying the names of clusters, sub-clusters, and/or cell subsets to include. If NULL, all available sets in obj are used.

show_pos_markers

Logical; whether to include positive markers. Default is TRUE.

show_neg_markers

Logical; whether to include negative markers. Default is FALSE.

show_med_markers

Logical; whether to include medium markers. Default is FALSE.

thresh_mode

Character; method for selecting top markers. One of:

"rank": include all markers up to the specified rank threshold.
"n": include exactly the top n markers.

thresh

Integer; threshold for selecting markers based on thresh_mode. Default is 5.

title

Optional character string for the plot title.

subtitle

Optional character string for the plot subtitle.

tag

Optional character string for the plot tag.

nrow_panels

Optional integer specifying the number of rows in the faceted plot. If NULL, rows are determined automatically.

dotsize

Numeric; size of the dots in the plot. Default is 2.

show_purity

Logical; if TRUE, dot color represents marker purity. If FALSE, dot color represents marker class. Default is TRUE.

class_palette

Optional palette used when show_purity = FALSE. Can be either:

A ggplot2 scale object (e.g., ggplot2::scale_fill_hue())
A character vector of colors

color_low

Character; low color for gradient (used when show_purity = TRUE). Default is "blue".

color_high

Character; high color for gradient (used when show_purity = TRUE). Default is "red".

panel_border_color

Character; color of panel borders.

panel_border_size

Numeric; size of panel borders.

axis_text_size

Numeric; font size for axis text.

axis_title_size

Numeric; font size for axis titles.

plot_margin_right

Numeric; right margin of the plot.

xlab

Character; label for the x-axis. Default is "Rank".

ylab

Character; label for the y-axis. Default is "Marker".

show_legend

Logical; whether to display the legend. Default is TRUE.

legend_box

Character; layout of the legend box (e.g., "vertical").

legend_box_just

Character; justification of the legend box.

legend_position

Character; position of the legend (e.g., "right").

Value

A ggplot2 object showing a faceted dot plot of selected markers across clusters, sub-clusters, or cell subsets.

Details

This function provides a flexible visualization for exploring marker genes identified in clustering analyses. Marker selection can be based on rank or a fixed number of top markers. The resulting plot is faceted by cluster or subset, enabling comparison across groups.

When show_purity = TRUE, a continuous color scale is used to represent marker purity. Otherwise, discrete colors are used to represent marker classes (e.g., positive, negative, medium).

Examples

if (FALSE) { # \dontrun{
# Example usage with a ClustoCell object
plt <- markoClustVis(
  obj = my_clustocell_object,
  desired_sets = c("Cluster1", "Cluster2"),
  show_pos_markers = TRUE,
  show_neg_markers = TRUE,
  thresh_mode = "n",
  thresh = 5,
  title = "Marker visualization"
)

print(plt)
} # }