Wrapper around heatmap_foldchange, which generates a heatmap of showing the foldchange for a set of gene expressions between specified groups. Differential gene expression analysis between the different groups can be performed.
Usage
DO.HeatmapFC(
sce_object,
features,
reference = NULL,
assay_normalized = "RNA",
group_by = "seurat_clusters",
condition_key = "condition",
groups_order = NULL,
conditions_order = NULL,
layer = NULL,
figsize = c(5, 6),
ax = NULL,
swap_axes = TRUE,
title = NULL,
title_fontproperties = list(size = NULL, weight = NULL),
palette = "RdBu_r",
palette_conditions = "tab10",
ticks_fontproperties = list(size = NULL, weight = NULL),
xticks_rotation = NULL,
yticks_rotation = NULL,
vmin = NULL,
vcenter = NULL,
vmax = NULL,
colorbar_legend_title = "Log2FC",
groups_legend_title = "Comparison",
group_legend_ncols = 1,
path = NULL,
filename = "Heatmap.svg",
showP = TRUE,
add_stats = TRUE,
test = c("wilcox"),
correction_method = c("bonferroni"),
df_pvals = NULL,
stats_x_size = NULL,
square_x_size = NULL,
pval_cutoff = 0.05,
log2fc_cutoff = 0,
linewidth = 0.1,
color_axis_ratio = 0.15
)Arguments
- sce_object
A SingleCellExperiment or Seurat object containing expression data and metadata.
- features
Character vector of gene names or metadata column names to be visualized.
- reference
Reference condition used for fold-change calculation.
- assay_normalized
Name of the assay containing normalized expression values (default: "RNA").
- group_by
Metadata column defining the primary grouping variable (e.g. clusters).
- condition_key
Metadata column defining the condition or comparison variable.
- groups_order
Optional character vector specifying the order of groups in
group_by.- conditions_order
Optional character vector specifying the order of conditions.
- layer
Optional layer name to extract expression values from.
- figsize
Numeric vector of length two specifying figure width and height.
- ax
Optional matplotlib axis object (for Python backend usage).
- swap_axes
Logical; whether to swap x- and y-axes.
- title
Optional title for the heatmap.
- title_fontproperties
Named list specifying font properties for the title (e.g. size, weight).
- palette
Color palette used for the heatmap.
- palette_conditions
Color palette used for condition annotations.
- ticks_fontproperties
Named list specifying font properties for axis tick labels.
- xticks_rotation
Rotation angle for x-axis tick labels.
- yticks_rotation
Rotation angle for y-axis tick labels.
- vmin
Minimum value for the color scale.
- vcenter
Center value for the color scale.
- vmax
Maximum value for the color scale.
- colorbar_legend_title
Title for the color bar.
- groups_legend_title
Title for the group legend.
- group_legend_ncols
Number of columns in the group legend.
- path
Optional path to save the output figure.
- filename
Name of the output file.
- showP
Logical; whether to display the plot.
- add_stats
Logical; whether to add statistical annotations.
- test
Statistical test to use (currently "wilcox").
- correction_method
Multiple-testing correction method (currently "bonferroni").
- df_pvals
Optional data frame containing precomputed p-values (groups x genes or genes x groups depending on axis orientation).
- stats_x_size
Size of the statistical annotation symbol.
- square_x_size
Size of the square annotation.
- pval_cutoff
P-value significance threshold.
- log2fc_cutoff
Minimum absolute log2 fold-change cutoff.
- linewidth
Line width of heatmap cell borders.
- color_axis_ratio
Relative size of the color bar axis.
Examples
sce_data <-
readRDS(system.file("extdata", "sce_data.rds", package = "DOtools"))
DO.HeatmapFC(
sce_object = sce_data,
features = c("HES4", "ISG15", "TNFRSF18", "TNFRSF4", "MMP23B"),
reference = NULL,
assay_normalized = "RNA",
group_by = "seurat_clusters",
condition_key = "condition",
groups_order = c("1", "2", "3", "4", "5", "6", "7", "8"),
conditions_order = NULL,
layer = NULL,
# Figure parameters
figsize = c(5, 6),
ax = NULL,
swap_axes = TRUE,
title = NULL,
title_fontproperties = list(size = NULL, weight = NULL),
palette = "RdBu_r",
palette_conditions = "tab10",
ticks_fontproperties = list(size = NULL, weight = NULL),
xticks_rotation = 45,
yticks_rotation = NULL,
vmin = NULL,
vcenter = NULL,
vmax = NULL,
colorbar_legend_title = "Log2FC",
groups_legend_title = "Comparison",
group_legend_ncols = 1,
# IO
path = NULL,
filename = "Heatmap.svg",
show = FALSE,
# # Statistics
add_stats = TRUE,
test = c("wilcox"),
correction_method = c("bonferroni"),
df_pvals = NULL,
stats_x_size = NULL,
square_x_size = NULL,
pval_cutoff = 0.05,
log2fc_cutoff = 0.0,
# Fx specific
linewidth = 0.1,
color_axis_ratio = 0.15
)
#> 2026-01-21 13:39:51 - reference is set to NULL, using: healthy