GroupHeatmap

GroupHeatmap

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,
  slot = "counts",
  assay = NULL,
  exp_method = c("zscore", "raw", "fc", "log2fc", "log1p"),
  exp_legend_title = NULL,
  limits = NULL,
  lib_normalize = identical(slot, "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 = unit(4, "in"),
  terms_fontsize = 8,
  keys_width = unit(2, "in"),
  keys_fontsize = c(6, 10),
  features_width = 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 = 103,
  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 = 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 = unit(10, "mm")) else list(height =
    unit(10, "mm")),
  feature_annotation = NULL,
  feature_annotation_palette = "Dark2",
  feature_annotation_palcolor = NULL,
  feature_annotation_params = if (flip) list(height = unit(5, "mm")) else list(width =
    unit(5, "mm")),
  use_raster = NULL,
  raster_device = "png",
  raster_by_magick = FALSE,
  height = NULL,
  width = NULL,
  units = "inch",
  seed = 11,
  ht_params = list()
)

Arguments

srt: A Seurat object.
features: The features to include in the heatmap.
group.by: A character vector specifying the groups to group by. Default is NULL.
split.by: A character vector specifying the variable to split the heatmap by. Default is NULL.
within_groups: A logical value indicating 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. The default value 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 specifying the cells to include in the heatmap. Default is NULL.
aggregate_fun: A function to use for aggregating data within groups. Default is base::mean.
exp_cutoff: A numeric value specifying the threshold for cell counting if add_dot is TRUE. Default is 0.
border: A logical value indicating whether to add a border to the heatmap. Default is TRUE.
flip: A logical value indicating whether to flip the heatmap. Default is FALSE.
slot: A character vector specifying the slot in the Seurat object to use. Default is "counts".
assay: A character vector specifying the assay in the Seurat object to use. Default is NULL.
exp_method: A character vector specifying the method for calculating expression values. Default is "zscore" with options "zscore", "raw", "fc", "log2fc", "log1p".
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: A logical value indicating 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: An integer specifying the 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. Default is "kmeans" with options "kmeans", "hclust", "mfuzz").
decreasing: A logical value indicating whether to sort feature splits in decreasing order. Default is FALSE.
fuzzification: A numeric value specifying 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: A logical value indicating whether to cluster rows in the heatmap. Default is FALSE.
cluster_columns: A logical value indicating whether to cluster columns in the heatmap. Default is FALSE.
cluster_row_slices: A logical value indicating whether to cluster row slices in the heatmap. Default is FALSE.
cluster_column_slices: A logical value indicating whether to cluster column slices in the heatmap. Default is FALSE.
show_row_names: A logical value indicating whether to show row names in the heatmap. Default is FALSE.
show_column_names: A logical value indicating 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: A numeric value specifying the rotation angle for row names. Default is 0.
column_names_rot: A numeric value specifying 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: A numeric value specifying the rotation angle for row title. Default is 0.
column_title_rot: A numeric value specifying the rotation angle for column title.
anno_terms: A logical value indicating whether to include term annotations. Default is FALSE.
anno_keys: A logical value indicating whether to include key annotations. Default is FALSE.
anno_features: A logical value indicating 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: A logical value indicating whether to update the database. Default is FALSE.
db_version: A character vector specifying the version of the database. Default is "latest".
db_combine: A logical value indicating whether to use a combined database. Default is FALSE.
convert_species: A logical value indicating whether to use a species-converted database if annotation is missing for species. Default is FALSE.
Ensembl_version: An integer specifying the Ensembl version. Default is 103.
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: A logical value indicating 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: A numeric value specifying 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: A numeric value specifying the adjusted p-value cutoff for significance. Default is 0.05.
topTerm: An integer specifying the number of top terms to include. Default is 5.
show_termid: A logical value indicating whether to show term IDs. Default is FALSE.
topWord: An integer specifying the number of top words to include. Default is 20.
words_excluded: A character vector specifying the words to exclude. Default is NULL.
nlabel: An integer specifying the number of labels to include. Default is 0.
features_label: A character vector specifying the features to label. Default is NULL.
label_size: A numeric value specifying the size of labels. Default is 10.
label_color: A character vector specifying the color of labels. Default is "black".
add_bg: A logical value indicating whether to add a background to the heatmap. Default is FALSE.
bg_alpha: A numeric value specifying the alpha value for the background color. Default is 0.5.
add_dot: A logical value indicating 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: A logical value indicating 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: A logical value indicating 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 an empty list.
use_raster: A logical value indicating 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: A logical value indicating 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: An integer specifying the random seed. Default is 11.
ht_params: A list specifying additional parameters passed to the ComplexHeatmap::Heatmap function. Default is an empty list.

Value

A list with the following elements:

plotThe heatmap plot.
matrix_listA list of matrix for each group.by used in the heatmap.
feature_splitNULL or a factor if splitting is performed in the heatmap.
cell_metadataMeta data of cells used to generate the heatmap.
cell_metadataMeta data of features used to generate the heatmap.
enrichmentNULL or a enrichment result generated by RunEnrichment when any of the parameters anno_terms, anno_keys, or anno_features is set to TRUE.

Examples

library(dplyr)
data("pancreas_sub")
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")
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
ht1$plot

panel_fix(ht1$plot, height = 4, width = 6, raster = TRUE, dpi = 50)
#> Error in panel_fix(ht1$plot, height = 4, width = 6, raster = TRUE, dpi = 50): unused arguments (height = 4, width = 6, raster = TRUE, dpi = 50)

pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType")
#> Warning: The following arguments are not used: drop
#> Warning: The following arguments are not used: drop
#> Error in as.vector(data): no method for coercing this S4 class to a vector
de_filter <- filter(pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox, p_val_adj < 0.05 & avg_log2FC > 1)
#> Error in UseMethod("filter"): no applicable method for 'filter' applied to an object of class "NULL"

ht2 <- GroupHeatmap(
  srt = pancreas_sub, features = de_filter$gene, group.by = "CellType",
  split.by = "Phase", cell_split_palette = "Dark2",
  cluster_rows = TRUE, cluster_columns = TRUE
)
#> Error: object 'de_filter' not found
ht2$plot
#> Error: object 'ht2' not found

ht3 <- GroupHeatmap(
  srt = 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
)
#> Error: object 'de_filter' not found
ht3$plot
#> Error: object 'ht3' not found

pancreas_sub <- AnnotateFeatures(pancreas_sub, species = "Mus_musculus", db = c("TF", "CSPA"))
#> Species: Mus_musculus
#> Preparing database: TF
#> Error in download(url = url, destfile = temp): could not find function "download"
de_top <- de_filter %>%
  group_by(gene) %>%
  top_n(1, avg_log2FC) %>%
  group_by(group1) %>%
  top_n(3, avg_log2FC)
#> Error: object 'de_filter' not found
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 = 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
)
#> Error: object 'de_top' not found
ht4$plot
#> Error: object 'ht4' not found

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 = 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
)
#> Error: object 'de_top' not found
ht5$plot
#> Error: object 'ht5' not found

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
)
#> Error: object 'de_top' not found
ht6$plot
#> Error: object 'ht6' not found

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
)
#> Error: object 'de_top' not found
ht7$plot
#> Error: object 'ht7' not found

ht8 <- GroupHeatmap(pancreas_sub,
  features = de_top$gene, group.by = "CellType", split.by = "Phase", n_split = 4,
  cluster_rows = TRUE, cluster_columns = TRUE, cluster_row_slices = TRUE, cluster_column_slices = TRUE,
  add_dot = TRUE, add_reticle = TRUE, heatmap_palette = "viridis",
  nlabel = 0, show_row_names = TRUE,
  ht_params = list(row_gap = unit(0, "mm"), row_names_gp = gpar(fontsize = 10))
)
#> Error: object 'de_top' not found
ht8$plot
#> Error: object 'ht8' not found

Usage

Arguments

Value

See also

Examples