The Group Heatmap

Usage

GroupHeatmap(
  srt,
  features = NULL,
  group.by = NULL,
  split.by = NULL,
  within_groups = FALSE,
  grouping.var = NULL,
  numerator = NULL,
  cells = NULL,
  aggregate_fun = base::mean,
  exp_cutoff = 0,
  border = TRUE,
  flip = FALSE,
  layer = "counts",
  assay = NULL,
  exp_method = c("zscore", "raw", "fc", "log2fc", "log1p"),
  exp_legend_title = NULL,
  limits = NULL,
  lib_normalize = identical(layer, "counts"),
  libsize = NULL,
  feature_split = NULL,
  feature_split_by = NULL,
  n_split = NULL,
  split_order = NULL,
  split_method = c("kmeans", "hclust", "mfuzz"),
  decreasing = FALSE,
  fuzzification = NULL,
  cluster_features_by = NULL,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  cluster_row_slices = FALSE,
  cluster_column_slices = FALSE,
  show_row_names = FALSE,
  show_column_names = FALSE,
  row_names_side = ifelse(flip, "left", "right"),
  column_names_side = ifelse(flip, "bottom", "top"),
  row_names_rot = 0,
  column_names_rot = 90,
  row_title = NULL,
  column_title = NULL,
  row_title_side = "left",
  column_title_side = "top",
  row_title_rot = 0,
  column_title_rot = ifelse(flip, 90, 0),
  anno_terms = FALSE,
  anno_keys = FALSE,
  anno_features = FALSE,
  terms_width = grid::unit(4, "in"),
  terms_fontsize = 8,
  keys_width = grid::unit(2, "in"),
  keys_fontsize = c(6, 10),
  features_width = grid::unit(2, "in"),
  features_fontsize = c(6, 10),
  IDtype = "symbol",
  species = "Homo_sapiens",
  db_update = FALSE,
  db_version = "latest",
  db_combine = FALSE,
  convert_species = TRUE,
  Ensembl_version = NULL,
  mirror = NULL,
  db = "GO_BP",
  TERM2GENE = NULL,
  TERM2NAME = NULL,
  minGSSize = 10,
  maxGSSize = 500,
  GO_simplify = FALSE,
  GO_simplify_cutoff = "p.adjust < 0.05",
  simplify_method = "Wang",
  simplify_similarityCutoff = 0.7,
  pvalueCutoff = NULL,
  padjustCutoff = 0.05,
  topTerm = 5,
  show_termid = FALSE,
  topWord = 20,
  words_excluded = NULL,
  nlabel = 20,
  features_label = NULL,
  label_size = 10,
  label_color = "black",
  add_bg = FALSE,
  bg_alpha = 0.5,
  add_dot = FALSE,
  dot_size = grid::unit(8, "mm"),
  add_reticle = FALSE,
  reticle_color = "grey",
  add_violin = FALSE,
  fill.by = "feature",
  fill_palette = "Dark2",
  fill_palcolor = NULL,
  heatmap_palette = "RdBu",
  heatmap_palcolor = NULL,
  group_palette = "Paired",
  group_palcolor = NULL,
  cell_split_palette = "simspec",
  cell_split_palcolor = NULL,
  feature_split_palette = "simspec",
  feature_split_palcolor = NULL,
  cell_annotation = NULL,
  cell_annotation_palette = "Paired",
  cell_annotation_palcolor = NULL,
  cell_annotation_params = if (flip) {
     list(width = grid::unit(10, "mm"))
 } else {

        list(height = grid::unit(10, "mm"))
 },
  feature_annotation = NULL,
  feature_annotation_palette = "Dark2",
  feature_annotation_palcolor = NULL,
  feature_annotation_params = if (flip) {
     list(height = grid::unit(5, "mm"))
 } else
    {
     list(width = grid::unit(5, "mm"))
 },
  use_raster = NULL,
  raster_device = "png",
  raster_by_magick = FALSE,
  height = NULL,
  width = NULL,
  units = "inch",
  seed = 11,
  ht_params = list(),
  verbose = TRUE,
  ...
)

Arguments

srt: A Seurat object.
features: A character vector of features to use. Default is NULL.
group.by: Name of one or more meta.data columns to group (color) cells by.
split.by: Name of a column in meta.data column to split plot by. Default is NULL.
within_groups: Whether to create separate heatmap scales for each group or within each group. Default is FALSE.
grouping.var: A character vector that specifies another variable for grouping, such as certain conditions. Default is NULL.
numerator: A character vector specifying the value to use as the numerator in the grouping.var grouping. Default is NULL.
cells: A character vector of cell names to use. Default is NULL.
aggregate_fun: A function to use for aggregating data within groups. Default is base::mean.
exp_cutoff: The threshold for cell counting if add_dot is TRUE. Default is 0.
border: Whether to add a border to the heatmap. Default is TRUE.
flip: Whether to flip the heatmap. Default is FALSE.
layer: Which layer to use. Default is "counts".
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used.
exp_method: A character vector specifying the method for calculating expression values. Options are "zscore", "raw", "fc", "log2fc", or "log1p". Default is "zscore".
exp_legend_title: A character vector specifying the title for the legend of expression value. Default is NULL.
limits: A two-length numeric vector specifying the limits for the color scale. Default is NULL.
lib_normalize: Whether to normalize the data by library size.
libsize: A numeric vector specifying the library size for each cell. Default is NULL.
feature_split: A factor specifying how to split the features. Default is NULL.
feature_split_by: A character vector specifying which group.by to use when splitting features (into n_split feature clusters). Default is NULL.
n_split: A number of feature splits (feature clusters) to create. Default is NULL.
split_order: A numeric vector specifying the order of splits. Default is NULL.
split_method: A character vector specifying the method for splitting features. Options are "kmeans", "hclust", or "mfuzz". Default is "kmeans".
decreasing: Whether to sort feature splits in decreasing order. Default is FALSE.
fuzzification: The fuzzification coefficient. Default is NULL.
cluster_features_by: A character vector specifying which group.by to use when clustering features. Default is NULL. By default, this parameter is set to NULL, which means that all groups will be used.
cluster_rows: Whether to cluster rows in the heatmap. Default is FALSE.
cluster_columns: Whether to cluster columns in the heatmap. Default is FALSE.
cluster_row_slices: Whether to cluster row slices in the heatmap. Default is FALSE.
cluster_column_slices: Whether to cluster column slices in the heatmap. Default is FALSE.
show_row_names: Whether to show row names in the heatmap. Default is FALSE.
show_column_names: Whether to show column names in the heatmap. Default is FALSE.
row_names_side: A character vector specifying the side to place row names.
column_names_side: A character vector specifying the side to place column names.
row_names_rot: The rotation angle for row names. Default is 0.
column_names_rot: The rotation angle for column names. Default is 90.
row_title: A character vector specifying the title for rows. Default is NULL.
column_title: A character vector specifying the title for columns. Default is NULL.
row_title_side: A character vector specifying the side to place row title. Default is "left".
column_title_side: A character vector specifying the side to place column title. Default is "top".
row_title_rot: The rotation angle for row title. Default is 0.
column_title_rot: The rotation angle for column title.
anno_terms: Whether to include term annotations. Default is FALSE.
anno_keys: Whether to include key annotations. Default is FALSE.
anno_features: Whether to include feature annotations. Default is FALSE.
terms_width: A unit specifying the width of term annotations. Default is unit(4, "in").
terms_fontsize: A numeric vector specifying the font size(s) for term annotations. Default is 8.
keys_width: A unit specifying the width of key annotations. Default is unit(2, "in").
keys_fontsize: A two-length numeric vector specifying the minimum and maximum font size(s) for key annotations. Default is c(6, 10).
features_width: A unit specifying the width of feature annotations. Default is unit(2, "in").
features_fontsize: A two-length numeric vector specifying the minimum and maximum font size(s) for feature annotations. Default is c(6, 10).
IDtype: A character vector specifying the type of IDs for features. Default is "symbol".
species: A character vector specifying the species for features. Default is "Homo_sapiens".
db_update: Whether the gene annotation databases should be forcefully updated. If set to FALSE, the function will attempt to load the cached databases instead. Default is FALSE.
db_version: A character vector specifying the version of the gene annotation databases to be retrieved. Default is "latest".
db_combine: Whether to use a combined database. Default is FALSE.
convert_species: Whether to use a species-converted database when the annotation is missing for the specified species. Default is TRUE.
Ensembl_version: An integer specifying the Ensembl version. Default is NULL. If NULL, the latest version will be used.
mirror: A character vector specifying the mirror for the Ensembl database. Default is NULL.
db: A character vector specifying the database to use. Default is "GO_BP".
TERM2GENE: A data.frame specifying the TERM2GENE mapping for the database. Default is NULL.
TERM2NAME: A data.frame specifying the TERM2NAME mapping for the database. Default is NULL.
minGSSize: An integer specifying the minimum gene set size for the database. Default is 10.
maxGSSize: An integer specifying the maximum gene set size for the database. Default is 500.
GO_simplify: Whether to simplify gene ontology terms. Default is FALSE.
GO_simplify_cutoff: A character vector specifying the cutoff for GO simplification. Default is "p.adjust < 0.05".
simplify_method: A character vector specifying the method for GO simplification. Default is "Wang".
simplify_similarityCutoff: The similarity cutoff for GO simplification. Default is 0.7.
pvalueCutoff: A numeric vector specifying the p-value cutoff(s) for significance. Default is NULL.
padjustCutoff: The adjusted p-value cutoff for significance. Default is 0.05.
topTerm: A number of top terms to include. Default is 5.
show_termid: Whether to show term IDs. Default is FALSE.
topWord: A number of top words to include. Default is 20.
words_excluded: A character vector specifying the words to exclude. Default is NULL.
nlabel: A number of labels to include. Default is 20.
features_label: A character vector specifying the features to label. Default is NULL.
label_size: The size of labels. Default is 10.
label_color: A character vector specifying the color of labels. Default is "black".
add_bg: Whether to add a background to the heatmap. Default is FALSE.
bg_alpha: The alpha value for the background color. Default is 0.5.
add_dot: Whether to add dots to the heatmap. The size of dot represents percentage of expressed cells based on the specified exp_cutoff. Default is FALSE.
dot_size: A unit specifying the base size of the dots. Default is unit(8, "mm").
add_reticle: Whether to add reticles to the heatmap. Default is FALSE.
reticle_color: A character vector specifying the color of the reticles. Default is "grey".
add_violin: Whether to add violins to the heatmap. Default is FALSE.
fill.by: A character vector specifying what to fill the violin. Possible values are "group", "feature", or "expression". Default is "feature".
fill_palette: A character vector specifying the palette to use for fill. Default is "Dark2".
fill_palcolor: A character vector specifying the fill color to use. Default is NULL.
heatmap_palette: A character vector specifying the palette to use for the heatmap. Default is "RdBu".
heatmap_palcolor: A character vector specifying the heatmap color to use. Default is NULL.
group_palette: A character vector specifying the palette to use for groups. Default is "Paired".
group_palcolor: A character vector specifying the group color to use. Default is NULL.
cell_split_palette: A character vector specifying the palette to use for cell splits. Default is "simspec".
cell_split_palcolor: A character vector specifying the cell split color to use. Default is NULL.
feature_split_palette: A character vector specifying the palette to use for feature splits. Default is "simspec".
feature_split_palcolor: A character vector specifying the feature split color to use. Default is NULL.
cell_annotation: A character vector specifying the cell annotation(s) to include. Default is NULL.
cell_annotation_palette: A character vector specifying the palette to use for cell annotations. The length of the vector should match the number of cell_annotation. Default is "Paired".
cell_annotation_palcolor: A list of character vector specifying the cell annotation color(s) to use. The length of the list should match the number of cell_annotation. Default is NULL.
cell_annotation_params: A list specifying additional parameters for cell annotations. Default is a list with width = unit(1, "cm") if flip is TRUE, else a list with height = unit(1, "cm").
feature_annotation: A character vector specifying the feature annotation(s) to include. Default is NULL.
feature_annotation_palette: A character vector specifying the palette to use for feature annotations. The length of the vector should match the number of feature_annotation. Default is "Dark2".
feature_annotation_palcolor: A list of character vector specifying the feature annotation color to use. The length of the list should match the number of feature_annotation. Default is NULL.
feature_annotation_params: A list specifying additional parameters for feature annotations. Default is list().
use_raster: Whether to use a raster device for plotting. Default is NULL.
raster_device: A character vector specifying the raster device to use. Default is "png".
raster_by_magick: Whether to use the 'magick' package for raster. Default is FALSE.
height: A numeric vector specifying the height(s) of the heatmap body. Default is NULL.
width: A numeric vector specifying the width(s) of the heatmap body. Default is NULL.
units: A character vector specifying the units for the height and width. Default is "inch".
seed: Random seed for reproducibility. Default is 11.
ht_params: Additional parameters to customize the appearance of the heatmap. This should be a list with named elements, where the names correspond to parameter names in the ComplexHeatmap::Heatmap function. Any conflicting parameters will override the defaults set by this function. Default is list().
verbose: Whether to print the message. Default is TRUE.
...: Additional arguments passed to the ComplexHeatmap::Heatmap function.

Value

A list with the following elements:

plot: The heatmap plot.
matrix_list: A list of matrix for each group.by used in the heatmap.
feature_split: NULL or a factor if splitting is performed in the heatmap.
cell_metadata: Meta data of cells used to generate the heatmap.
feature_metadata: Meta data of features used to generate the heatmap.
enrichment: NULL or a enrichment result generated by RunEnrichment when any of the parameters anno_terms, anno_keys, or anno_features is set to TRUE.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2026-01-27 07:51:25] Start standard scop workflow...
#> ℹ [2026-01-27 07:51:26] Checking a list of <Seurat>...
#> ! [2026-01-27 07:51:26] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-01-27 07:51:26] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-27 07:51:27] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-27 07:51:28] Use the separate HVF from srt_list
#> ℹ [2026-01-27 07:51:28] Number of available HVF: 2000
#> ℹ [2026-01-27 07:51:28] Finished check
#> ℹ [2026-01-27 07:51:29] Perform `Seurat::ScaleData()`
#> ℹ [2026-01-27 07:51:29] Perform pca linear dimension reduction
#> ℹ [2026-01-27 07:51:30] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-01-27 07:51:30] Reorder clusters...
#> ℹ [2026-01-27 07:51:30] Perform umap nonlinear dimension reduction
#> ℹ [2026-01-27 07:51:30] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2026-01-27 07:51:34] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ✔ [2026-01-27 07:51:37] Run scop standard workflow completed
ht1 <- GroupHeatmap(
  pancreas_sub,
  features = c(
    "Sox9", "Anxa2", "Bicc1", # Ductal
    "Neurog3", "Hes6", # EPs
    "Fev", "Neurod1", # Pre-endocrine
    "Rbp4", "Pyy", # Endocrine
    "Ins1", "Gcg", "Sst", "Ghrl"
    # Beta, Alpha, Delta, Epsilon
  ),
  group.by = c("CellType", "SubCellType")
)
ht1$plot


thisplot::panel_fix(
  ht1$plot,
  height = 4,
  width = 6,
  raster = TRUE,
  dpi = 50
)


if (FALSE) { # \dontrun{
library(dplyr)
pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  species = "Mus_musculus",
  db = c("CSPA", "TF")
)
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType"
)
de_filter <- filter(
  pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox,
  p_val_adj < 0.05 & avg_log2FC > 1
)

ht2 <- GroupHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  group.by = "CellType",
  split.by = "Phase",
  cell_split_palette = "Dark2",
  cluster_rows = TRUE,
  cluster_columns = TRUE
)
ht2$plot

ht3 <- GroupHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  feature_split = de_filter$group1,
  group.by = "CellType",
  species = "Mus_musculus",
  db = "GO_BP",
  anno_terms = TRUE,
  anno_keys = TRUE,
  anno_features = TRUE
)
ht3$plot

de_top <- de_filter %>%
  group_by(gene) %>%
  top_n(1, avg_log2FC) %>%
  group_by(group1) %>%
  top_n(3, avg_log2FC)
ht4 <- GroupHeatmap(
  pancreas_sub,
  features = de_top$gene,
  feature_split = de_top$group1,
  group.by = "CellType",
  heatmap_palette = "YlOrRd",
  cell_annotation = c(
    "Phase", "G2M_score", "Neurod2"
  ),
  cell_annotation_palette = c(
    "Dark2", "Paired", "Paired"
  ),
  cell_annotation_params = list(
    height = grid::unit(10, "mm")
  ),
  feature_annotation = c("TF", "CSPA"),
  feature_annotation_palcolor = list(
    c("gold", "steelblue"),
    c("forestgreen")
  ),
  add_dot = TRUE,
  add_bg = TRUE,
  nlabel = 0,
  show_row_names = TRUE
)
ht4$plot

ht5 <- GroupHeatmap(
  pancreas_sub,
  features = de_top$gene,
  feature_split = de_top$group1,
  group.by = "CellType",
  heatmap_palette = "YlOrRd",
  cell_annotation = c(
    "Phase", "G2M_score", "Neurod2"
  ),
  cell_annotation_palette = c(
    "Dark2", "Paired", "Paired"
  ),
  cell_annotation_params = list(
    width = grid::unit(10, "mm")
  ),
  feature_annotation = c("TF", "CSPA"),
  feature_annotation_palcolor = list(
    c("gold", "steelblue"), c("forestgreen")
  ),
  add_dot = TRUE,
  add_bg = TRUE,
  flip = TRUE,
  column_title_rot = 45,
  nlabel = 0,
  show_row_names = TRUE
)
ht5$plot

ht6 <- GroupHeatmap(
  pancreas_sub,
  features = de_top$gene,
  feature_split = de_top$group1,
  group.by = "CellType",
  add_violin = TRUE,
  cluster_rows = TRUE,
  nlabel = 0,
  show_row_names = TRUE
)
ht6$plot

ht7 <- GroupHeatmap(
  pancreas_sub,
  features = de_top$gene,
  feature_split = de_top$group1,
  group.by = "CellType",
  add_violin = TRUE,
  fill.by = "expression",
  fill_palette = "Blues",
  cluster_rows = TRUE,
  nlabel = 0,
  show_row_names = TRUE
)
ht7$plot

ht8 <- GroupHeatmap(
  pancreas_sub,
  features = de_top$gene,
  group.by = "CellType",
  split.by = "Phase",
  n_split = 4,
  cluster_rows = TRUE,
  cluster_columns = TRUE,
  cluster_row_slices = TRUE,
  cluster_column_slices = TRUE,
  add_dot = TRUE,
  add_reticle = TRUE,
  heatmap_palette = "viridis",
  nlabel = 0,
  show_row_names = TRUE,
  ht_params = list(
    row_gap = grid::unit(0, "mm"),
    row_names_gp = grid::gpar(fontsize = 10)
  )
)
ht8$plot
} # }

The Group Heatmap

Usage

Arguments

Value

See also

Examples