SingleCellComplexHeatMap (version 0.1.2)

create_cell_annotations: Create Cell Type and Time Point Annotations for Heatmap Columns

Description

Parses column names to extract time points and cell types, creates annotations and reorders matrices.

Usage

create_cell_annotations(
  exp_mat,
  percent_mat,
  split_pattern = "_",
  time_position = 1,
  celltype_start = 2,
  time_points_order = NULL,
  cell_types_order = NULL,
  time_color_palette = "Accent",
  celltype_color_palette = "Dark2",
  show_time_annotation = TRUE,
  show_celltype_annotation = TRUE,
  time_point_title = "Time Point",
  cell_type_title = "Cell Type"
)

Value

A list containing exp_mat_ordered (reordered expression matrix), percent_mat_ordered (reordered percentage matrix), col_annotation (ComplexHeatmap column annotation object), col_split_factor (factor for column splitting based on time points), and annotation_df (data frame with column annotations).

Arguments

exp_mat

Expression matrix with samples as columns

percent_mat

Percentage matrix with samples as columns

split_pattern

Character string used to split column names (default: "_")

time_position

Integer indicating position of time point in split names (default: 1)

celltype_start

Integer indicating starting position of cell type in split names (default: 2)

time_points_order

Character vector specifying order of time points (default: NULL for automatic)

cell_types_order

Character vector specifying order of cell types (default: NULL for automatic)

time_color_palette

Character string specifying palette name OR character vector of colors for time points (default: "Accent")

celltype_color_palette

Character string specifying palette name OR character vector of colors for cell types (default: "Dark2")

show_time_annotation

Logical indicating whether to show time point annotation (default: TRUE)

show_celltype_annotation

Logical indicating whether to show cell type annotation (default: TRUE)

time_point_title

Character string for time point annotation title (default: "Time Point")

cell_type_title

Character string for cell type annotation title (default: "Cell Type")

See Also

create_single_cell_complex_heatmap, prepare_expression_matrices

Examples

# Load a small example Seurat object
data("pbmc_small", package = "SeuratObject")
pbmc_small$timepoint <- sample(c("0h", "6h"), ncol(pbmc_small), replace = TRUE)
pbmc_small$timepoint_celltype <- paste(pbmc_small$timepoint, pbmc_small$RNA_snn_res.0.8, sep = "_")
features <- c("CD3D", "CD79A", "MS4A1")

# Prepare expression matrices first
matrices <- prepare_expression_matrices(pbmc_small, features, group_by = "timepoint_celltype")

# Create cell annotations with custom ordering
col_annotations <- create_cell_annotations(
  exp_mat = matrices$exp_mat,
  percent_mat = matrices$percent_mat,
  split_pattern = "_",
  time_points_order = c("0h", "6h"),
  cell_types_order = levels(pbmc_small$RNA_snn_res.0.8)
)

# Access results
ordered_exp_mat <- col_annotations$exp_mat_ordered