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Group heatmap

Source: R/GroupHeatmap.R
GroupHeatmap.Rd

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,
  heatmap_border = NULL,
  cell_annotation_border = NULL,
  feature_annotation_border = NULL,
  heatmap_border_palcolor = "black",
  cell_annotation_border_palcolor = "black",
  feature_annotation_border_palcolor = "black",
  heatmap_border_size = 1,
  cell_annotation_border_size = 1,
  feature_annotation_border_size = 1,
  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,
  row_names_wrap = NULL,
  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_stat_width = grid::unit(1.35, "in"),
  terms_fontsize = 8,
  terms_stat = "none",
  terms_stat_digits = 2,
  terms_stat_label = "value",
  terms_stat_axis = FALSE,
  terms_stat_background_palcolor = NULL,
  terms_stat_border = NULL,
  terms_stat_border_palcolor = NULL,
  terms_stat_border_size = NULL,
  terms_stat_label_palcolor = NULL,
  terms_group_background = FALSE,
  terms_background_palcolor = "grey98",
  terms_background_alpha = 1,
  terms_border = TRUE,
  terms_border_palcolor = "black",
  terms_border_size = 0.8,
  terms_text_palcolor = NULL,
  terms_bar_palcolor = NULL,
  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 = "Chinese",
  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 = "Chinese",
  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",
  cores = 1,
  seed = 11,
  legend.position = "right",
  ht_params = list(),
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object.

features

Features to plot.

group.by

Metadata column(s) used to color cells.

split.by

Metadata column to facet by.

within_groups

Separate color scales per group.

grouping.var, numerator

Extra grouping variable (e.g. condition) and the level used as numerator.

cells

Cell names to include.

aggregate_fun

Function used to aggregate expression within groups.

exp_cutoff

Expression cutoff for cell counting when add_dot = TRUE.

border

Draw borders. Kept for compatibility; more specific *_border arguments inherit this when NULL.

heatmap_border, cell_annotation_border, feature_annotation_border

Borders for the heatmap body and annotations. NULL inherits border.

heatmap_border_palcolor, cell_annotation_border_palcolor, feature_annotation_border_palcolor

Border colors when the matching border argument is TRUE.

heatmap_border_size, cell_annotation_border_size, feature_annotation_border_size

Border line widths when the matching border argument is TRUE.

flip

Flip rows and columns.

layer

Assay layer to use.

assay

Assay to use. NULL uses the default assay.

exp_method

Expression transform: "zscore", "raw", "fc", "log2fc", or "log1p".

exp_legend_title

Legend title for expression.

limits

Color-scale limits (length 2).

lib_normalize, libsize

Library-size normalization and per-cell library sizes.

feature_split, feature_split_by, n_split, split_order, split_method, decreasing

Feature splitting. split_method is "kmeans", "hclust", or "mfuzz".

fuzzification

Mfuzz fuzzification coefficient.

cluster_features_by

Grouping used when clustering features. NULL uses all groups.

cluster_rows, cluster_columns, cluster_row_slices, cluster_column_slices

Heatmap clustering.

show_row_names, show_column_names, row_names_wrap

Show names. row_names_wrap wraps displayed names (underscores as spaces) without changing feature IDs.

row_names_side, column_names_side, row_names_rot, column_names_rot

Name placement.

row_title, column_title, row_title_side, column_title_side, row_title_rot, column_title_rot

Slice titles.

anno_terms, anno_keys, anno_features

Enrichment annotations.

terms_width, terms_stat_width, terms_fontsize

Term annotation size.

terms_stat

Enrichment statistic for term bars: "none", "score" (-log10 of the active p-value), or an enrichment column such as "p.adjust".

terms_stat_digits, terms_stat_label, terms_stat_axis

Statistic labels ("none", "value", "significance", "both") and shared axis.

terms_stat_background_palcolor, terms_stat_border, terms_stat_border_palcolor, terms_stat_border_size, terms_stat_label_palcolor

Statistic-panel appearance. NULL inherits the matching terms_* setting.

terms_group_background, terms_background_palcolor, terms_background_alpha, terms_border, terms_border_palcolor, terms_border_size, terms_text_palcolor, terms_bar_palcolor

Term-block appearance. terms_text_palcolor = NULL maps text to enrichment significance; terms_bar_palcolor = NULL matches bar color to term text.

keys_width, keys_fontsize, features_width, features_fontsize

Key and feature annotations.

IDtype, species, db_combine, mirror, db, TERM2GENE, TERM2NAME, minGSSize, maxGSSize

Gene-set database (see PrepareDB).

db_update

Force a refresh. FALSE loads the cache when available.

db_version

Database version to retrieve.

convert_species

Use a species-converted database when the annotation is missing for species.

Ensembl_version

Ensembl version. NULL uses the latest.

GO_simplify, GO_simplify_cutoff, simplify_method, simplify_similarityCutoff

GO simplification.

pvalueCutoff, padjustCutoff, topTerm, show_termid, topWord, words_excluded

Enrichment filters.

nlabel, features_label, label_size, label_color

Feature labels.

add_bg, bg_alpha

Split-group background.

add_dot, dot_size

Dots sized by the fraction of cells above exp_cutoff.

add_reticle, reticle_color

Cell reticles.

add_violin, fill.by, fill_palette, fill_palcolor

Overlay violins. fill.by is "group", "feature", or "expression".

heatmap_palette, heatmap_palcolor, group_palette, group_palcolor

Heatmap and group colors.

cell_split_palette, cell_split_palcolor, feature_split_palette, feature_split_palcolor

Split colors.

cell_annotation, cell_annotation_palette, cell_annotation_palcolor, cell_annotation_params

Cell annotations. Palette length should match cell_annotation.

feature_annotation, feature_annotation_palette, feature_annotation_palcolor, feature_annotation_params

Feature annotations. Palette length should match feature_annotation.

use_raster, raster_device, raster_by_magick

Raster device (NULL chooses automatically).

width, height, units

Heatmap size. NULL sizes from matrix dimensions.

cores

The number of worker processes to use for parallelization. Default is 1.

seed

Optional integer seed. When supplied, every input receives a deterministic independent L'Ecuyer-CMRG random-number stream, making results reproducible across worker counts and scheduling order. The caller's random number state is restored when the call finishes.

legend.position

Legend side ("right", "left", "top", "bottom"). Gap to the heatmap grows automatically when long row names are on the right.

ht_params

Extra arguments passed to ComplexHeatmap::Heatmap, overriding defaults.

verbose

Whether to print the message. Default is TRUE.

...

Additional arguments passed to helper functions.

Value

A list with plot, matrix_list, feature_split, cell_metadata, feature_metadata, and enrichment (from RunEnrichment when term/key/feature annotations are requested).

See also

RunDEtest

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:31:36] Start standard processing workflow...
#> ℹ [2026-08-30 04:31:36] Checking a list of <Seurat>...
#> ! [2026-08-30 04:31:36] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:31:36] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:31:36] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:31:36] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:31:37] Number of available HVF: 2000
#> ℹ [2026-08-30 04:31:37] Finished check
#> ℹ [2026-08-30 04:31:37] Perform `ScaleData()`
#> ℹ [2026-08-30 04:31:37] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:31:37] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:31:37] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:31:37] Reorder clusters...
#> ℹ [2026-08-30 04:31:37] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:31:37] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:31:45] Standard processing 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
)


pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  species = "Mus_musculus",
  db = c("CSPA", "TF")
)
#> ℹ [2026-08-30 04:31:45] Species: "Mus_musculus"
#> ℹ [2026-08-30 04:31:45] Loading cached: CSPA version: CSPA nterm:1 created: 2026-08-30 04:23:52
#> ℹ [2026-08-30 04:31:46] Loading cached: TF version: AnimalTFDB4 nterm:2 created: 2026-08-30 04:00:31
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType"
)
#> ℹ [2026-08-30 04:31:47] Data type is log-normalized
#> ℹ [2026-08-30 04:31:47] Start differential expression test
#> ℹ [2026-08-30 04:31:47] Find all markers(wilcox) among [1] 5 groups...
#> ✔ [2026-08-30 04:31:48] Differential expression test completed
de_filter <- dplyr::filter(
  pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox,
  p_val_adj < 0.05 & avg_log2FC > 1
)

ht2 <- GroupHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  group.by = "CellType",
  split.by = "Phase",
  cell_split_palette = "Dark2",
  cluster_rows = TRUE,
  cluster_columns = TRUE
)
#> `use_raster` is automatically set to TRUE for a matrix with more than
#> 2000 rows. You can control `use_raster` argument by explicitly setting
#> TRUE/FALSE to it.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
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
)
#> ℹ [2026-08-30 04:31:53] Start Enrichment analysis
#> ℹ [2026-08-30 04:31:53] Species: "Mus_musculus"
#> ℹ [2026-08-30 04:31:53] Loading cached: GO_BP version: 3.23.0 nterm:14957 created: 2026-08-30 04:25:22
#> ℹ [2026-08-30 04:31:54] Permform enrichment...
#> ℹ [2026-08-30 04:31:55] Using 1 core
#> ⠙ [2026-08-30 04:31:55] Running for 1 [1/5] ■■          20% | ETA:  6s
#> ⠹ [2026-08-30 04:31:55] Running for 2 [2/5] ■■■■        40% | ETA:  5s
#> ⠸ [2026-08-30 04:31:55] Running for 4 [4/5] ■■■■■■■■    80% | ETA:  2s
#> ✔ [2026-08-30 04:31:55] Completed 5 tasks in 7.5s
#> 
#> ℹ [2026-08-30 04:31:55] Building results
#> ✔ [2026-08-30 04:32:03] Enrichment analysis done
#> ℹ [2026-08-30 04:32:44] The size of the heatmap is fixed because certain elements are not scalable.
#> ℹ [2026-08-30 04:32:44] The width and height of the heatmap are determined by the size of the current viewport.
#> ℹ [2026-08-30 04:32:44] If you want to have more control over the size, you can manually set the parameters 'width' and 'height'.
ht3$plot


de_top <- de_filter |>
  dplyr::group_by(gene) |>
  dplyr::top_n(1, avg_log2FC) |>
  dplyr::group_by(group1) |>
  dplyr::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", "Chinese", "Chinese"
  ),
  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
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
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", "Chinese", "Chinese"
  ),
  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
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
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
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's colour values.
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