Feature Heatmap

Feature Heatmap

Usage

FeatureHeatmap(
  srt,
  features = NULL,
  cells = NULL,
  group.by = NULL,
  split.by = NULL,
  within_groups = FALSE,
  max_cells = 100,
  cell_order = NULL,
  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 = FALSE,
  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",
  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(5, "mm"))
 } else {
 
       list(height = grid::unit(5, "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: A character vector of features to use. Default is NULL.
cells: A character vector of cell names 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.
max_cells: An integer, maximum number of cells to sample per group. Default is 100.
cell_order: A vector of cell names defining the order of cells. Default is NULL.
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. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
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".
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 "Chinese".
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 "Chinese".
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: The height of the heatmap in the specified units. If not provided, the height will be automatically determined based on the number of rows in the heatmap and the default unit.
width: The width of the heatmap in the specified units. If not provided, the width will be automatically determined based on the number of columns in the heatmap and the default unit.
units: The units to use for the width and height of the heatmap. Default is "inch", Options are "mm", "cm", or "inch".
cores: The number of cores to use for parallelization with foreach::foreach. Default is 1.
seed: Random seed for reproducibility. Default is 11.
legend.position: A character vector specifying the side to place the legends. Options are "right", "left", "top", or "bottom". Default is "right". When row names are long and shown on the right side, the gap between the heatmap and the legend is automatically increased to avoid overlap.
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 other functions.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType"
)
de_filter <- dplyr::filter(
  pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox,
  p_val_adj < 0.05 & avg_log2FC > 1
)
ht1 <- FeatureHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  group.by = "CellType",
  split.by = "Phase",
  cell_split_palette = "Dark2"
)
ht1$plot

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

ht2 <- FeatureHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  group.by = c("CellType", "SubCellType"),
  n_split = 4,
  cluster_rows = TRUE,
  cluster_row_slices = TRUE,
  cluster_columns = TRUE,
  cluster_column_slices = TRUE,
  ht_params = list(row_gap = grid::unit(0, "mm")),
  use_raster = FALSE
)
ht2$plot

ht3 <- FeatureHeatmap(
  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

pancreas_sub <- RunSlingshot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP"
)
ht4 <- FeatureHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  nlabel = 10,
  cell_order = names(sort(pancreas_sub$Lineage1)),
  cell_annotation = c("SubCellType", "Lineage1"),
  cell_annotation_palette = c("Chinese", "cividis")
)
ht4$plot

pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  species = "Mus_musculus",
  db = c("CSPA", "TF")
)

ht5 <- FeatureHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  n_split = 4,
  group.by = "CellType",
  heatmap_palette = "viridis",
  feature_annotation = c("TF", "CSPA"),
  feature_annotation_palcolor = list(
    c("gold", "steelblue"), c("forestgreen")
  ),
  cell_annotation = c("Phase", "G2M_score"),
  cell_annotation_palette = c("Dark2", "Purples")
)
ht5$plot

ht6 <- FeatureHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  n_split = 4,
  group.by = "CellType",
  heatmap_palette = "viridis",
  feature_annotation = c("TF", "CSPA"),
  feature_annotation_palcolor = list(
    c("gold", "steelblue"), c("forestgreen")
  ),
  cell_annotation = c("Phase", "G2M_score"),
  cell_annotation_palette = c("Dark2", "Purples"),
  flip = TRUE,
  column_title_rot = 45
)
ht6$plot

Usage

Arguments

See also

Examples