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Visualize per-signature marker expression across clusters

Source: R/signatureDotHeatmap.R
signatureDotHeatmap.Rd

Generates a dot heatmap summarizing expression of signature-associated features across clusters.

Usage

signatureDotHeatmap(
  seurat_obj,
  cluster_col,
  row_data,
  features_col = NULL,
  signature_col = NULL,
  cell_type_colors = NULL,
  signature_colors = NULL,
  tag = NULL,
  tile_palette = RColorBrewer::brewer.pal(9, "YlOrRd"),
  tile_alpha_range = c(0.15, 0.65),
  dot_size_factor = 2,
  dot_range = c(0.5, 3),
  signature_label_size = 3.3,
  feature_label_size = 6,
  feature_label_angle = 45,
  show_cluster_labels = FALSE,
  show_signature_strip = TRUE,
  show_signature_labels = TRUE,
  show_cluster_strip = TRUE,
  show_cluster_legend = TRUE,
  show_signature_legend = FALSE,
  legend_ncol = 2,
  expression_legend_title = "Expression",
  percent_legend_title = "Percent\nExpressed",
  tile_fill_legend_title = NULL,
  signature_legend_title = "Signature",
  vline_color = "black",
  vline_width = 0.15,
  block_border_color = "grey90",
  feature_label_face = "plain"
)

Arguments

seurat_obj

A Seurat object containing expression data and metadata.

cluster_col

Character; column in seurat_obj@meta.data containing cluster labels. These could correspond to user defined clusters or cell types.

row_data

Data frame mapping features to signatures. Must contain one row per feature.

features_col

Character; column in row_data containing feature (e.g. gene) IDs corresponding to the row names of the seurat_obj.

signature_col

Character; column in row_data containing signature labels.

cell_type_colors

Color specification for cell types.

signature_colors

Color specification for signatures.

tag

Optional plot tag.

tile_palette

Character vector defining tile fill colors.

tile_alpha_range

Numeric vector of length two defining alpha range.

dot_size_factor

Numeric; scaling factor for dot sizes.

dot_range

Numeric vector defining minimum and maximum dot sizes.

signature_label_size

Numeric; font size of signature labels.

feature_label_size

Numeric; font size of feature labels.

feature_label_angle

Numeric; angle of feature labels.

show_cluster_labels

Logical; whether to show cluster labels.

show_signature_strip

Logical; whether to show signature strip.

show_signature_labels

Logical; whether to show signature labels.

show_cluster_strip

Logical; whether to show cluster strip.

show_cluster_legend

Logical; whether to show cluster legend.

show_signature_legend

Logical; whether to show signature legend.

legend_ncol

Integer; number of legend columns.

expression_legend_title

Character; title for expression legend.

percent_legend_title

Character; title for percent expressed legend.

tile_fill_legend_title

Character; title for tile fill legend.

signature_legend_title

Character; title for signature legend.

vline_color

Character; color of vertical separator lines.

vline_width

Numeric; width of vertical separator lines.

block_border_color

Character; color of block borders.

feature_label_face

Character; font face for feature labels.

Value

A ggplot2 object.

Details

Dot size typically encodes the percentage of cells expressing a feature, while color intensity reflects average expression.

See also

typoClustVis, markoCell

Examples

if (FALSE) { # \dontrun{
p <- signatureDotHeatmap(
  seurat_obj = so,
  row_data = signatures,
  features_col = "Features",
  signature_col = "Signature"
)
} # }