Skip to contents

GroupHeatmap

Source: R/SCP-plot.R
GroupHeatmap.Rd

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.

See also

RunDEtest

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)


pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType")
#> Warning: Data in the 'data' slot is raw counts. Perform NormalizeData(LogNormalize) on the data.
#> [2023-11-21 07:21:22.592122] Start DEtest
#> Workers: 2
#> Find all markers(wilcox) among 5 groups...
#> 
  |                                                                                                                    
  |                                                                                                              |   0%
#> 
#> 
#> 
  |                                                                                                                    
  |============================================                                                                  |  40%
#> 
#> 
#> 
#> 
  |                                                                                                                    
  |==============================================================================================================| 100%
#> 
#> [2023-11-21 07:21:32.613376] DEtest done
#> Elapsed time:10.02 secs
de_filter <- filter(pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox, p_val_adj < 0.05 & avg_log2FC > 1)

ht2 <- GroupHeatmap(
  srt = pancreas_sub, features = de_filter$gene, group.by = "CellType",
  split.by = "Phase", cell_split_palette = "Dark2",
  cluster_rows = TRUE, cluster_columns = TRUE
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
#> `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(
  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
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
#> [2023-11-21 07:21:43.521111] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: GO_BP version:3.17.0 nterm:16027 created:2023-11-21 07:14:20.545084
#> Convert ID types for the database: GO_BP
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
ht3$plot
#> Error in eval(expr, envir, enclos): object 'ht3' not found

pancreas_sub <- AnnotateFeatures(pancreas_sub, species = "Mus_musculus", db = c("TF", "CSPA"))
#> Species: Mus_musculus
#> Loading cached db: TF version:AnimalTFDB4 nterm:2 created:2023-11-21 07:05:33.872428
#> Loading cached db: CSPA version:CSPA nterm:1 created:2023-11-21 07:05:36.02141
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 = 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
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
ht4$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 = 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
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
ht5$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
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
ht6$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
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
ht7$plot


ht8 <- GroupHeatmap(pancreas_sub,
  features = de_top$gene, group.by = "CellType", split.by = "Phase", n_split = 4,
  cluster_rows = TRUE, cluster_columns = TRUE, cluster_row_slices = TRUE, cluster_column_slices = TRUE,
  add_dot = TRUE, add_reticle = TRUE, heatmap_palette = "viridis",
  nlabel = 0, show_row_names = TRUE,
  ht_params = list(row_gap = unit(0, "mm"), row_names_gp = gpar(fontsize = 10))
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
ht8$plot