Generates a heatmap of gene-family expression across cells, optionally ordered by pseudotime and annotated by metadata.
Usage
generate_cell_heatmap(
expression_matrix,
gene_family_list,
metadata_df,
metadata_name = NULL,
legend_name = "",
apply_scale = TRUE,
k_smooth = 30,
cap = 20,
axis_text_size = 10,
discrete_colour_list = NULL,
continuous_colors = NULL,
show_pseudotime_legend = FALSE,
show_metadata_legend = TRUE,
show_modules_legend = FALSE,
show_expression_legend = TRUE
)Arguments
- expression_matrix
A gene-by-cell expression matrix.
- gene_family_list
A named list of genes grouped by gene family.
- metadata_df
A data frame with cell metadata; rownames must match cell names in
expression_matrix.- metadata_name
Optional metadata column used for the top annotation.
- legend_name
Title used for the heatmap legend.
- apply_scale
Logical indicating whether to z-score each gene across cells before plotting.
- k_smooth
Integer kernel size used to smooth expression along cells.
- cap
Numeric cap applied to scaled or raw expression values.
- axis_text_size
Font size used for row labels and annotations.
- discrete_colour_list
Optional named list of discrete colour vectors.
- continuous_colors
Optional vector of colors used for the heatmap body.
- show_pseudotime_legend
Logical indicating whether to show the pseudotime legend. Defaults to FALSE.
- show_metadata_legend
Logical indicating whether to show the metadata legend. Defaults to TRUE.
- show_modules_legend
Logical indicating whether to show the gene family legend. Defaults to FALSE.
- show_expression_legend
Logical indicating whether to show the expression legend. Defaults to TRUE.