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 = "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(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",
  seed = 11,
  ht_params = list()
)

Arguments

srt

A Seurat object.

features

The features to include in the heatmap. Default is NULL.

cells

A character vector specifying the cells to include in the heatmap. Default is NULL.

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

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

A character vector specifying the layer 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. 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 to update the database. Default is FALSE.

db_version

A character vector specifying the version of the database. Default is "latest".

db_combine

Whether to use a combined database. Default is FALSE.

convert_species

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

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 0.

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 "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

An integer specifying the random seed. Default is 11.

ht_params

A list specifying additional parameters passed to the ComplexHeatmap::Heatmap function. Default is list().

See also

RunDEtest

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> StandardPC_ 1 
#> Positive:  Aplp1, Cpe, Gnas, Fam183b, Map1b, Hmgn3, Pcsk1n, Chga, Tuba1a, Bex2 
#> 	   Syt13, Isl1, 1700086L19Rik, Pax6, Chgb, Scgn, Rbp4, Scg3, Gch1, Camk2n1 
#> 	   Cryba2, Pcsk2, Pyy, Tspan7, Mafb, Hist3h2ba, Dbpht2, Abcc8, Rap1b, Slc38a5 
#> Negative:  Spp1, Anxa2, Sparc, Dbi, 1700011H14Rik, Wfdc2, Gsta3, Adamts1, Clu, Mgst1 
#> 	   Bicc1, Ldha, Vim, Cldn3, Cyr61, Rps2, Mt1, Ptn, Phgdh, Nudt19 
#> 	   Smtnl2, Smco4, Habp2, Mt2, Col18a1, Rpl12, Galk1, Cldn10, Acot1, Ccnd1 
#> StandardPC_ 2 
#> Positive:  Rbp4, Tagln2, Tuba1b, Fkbp2, Pyy, Pcsk2, Iapp, Tmem27, Meis2, Tubb4b 
#> 	   Pcsk1n, Dbpht2, Rap1b, Dynll1, Tubb2a, Sdf2l1, Scgn, 1700086L19Rik, Scg2, Abcc8 
#> 	   Atp1b1, Hspa5, Fam183b, Papss2, Slc38a5, Scg3, Mageh1, Tspan7, Ppp1r1a, Ociad2 
#> Negative:  Neurog3, Btbd17, Gadd45a, Ppp1r14a, Neurod2, Sox4, Smarcd2, Mdk, Pax4, Btg2 
#> 	   Sult2b1, Hes6, Grasp, Igfbpl1, Gpx2, Cbfa2t3, Foxa3, Shf, Mfng, Tmsb4x 
#> 	   Amotl2, Gdpd1, Cdc14b, Epb42, Rcor2, Cotl1, Upk3bl, Rbfox3, Cldn6, Cer1 
#> StandardPC_ 3 
#> Positive:  Nusap1, Top2a, Birc5, Aurkb, Cdca8, Pbk, Mki67, Tpx2, Plk1, Ccnb1 
#> 	   2810417H13Rik, Incenp, Cenpf, Ccna2, Prc1, Racgap1, Cdk1, Aurka, Cdca3, Hmmr 
#> 	   Spc24, Kif23, Sgol1, Cenpe, Cdc20, Hist1h1b, Cdca2, Mxd3, Kif22, Ska1 
#> Negative:  Anxa5, Pdzk1ip1, Acot1, Tpm1, Anxa2, Dcdc2a, Capg, Sparc, Ttr, Pamr1 
#> 	   Clu, Cxcl12, Ndrg2, Hnf1aos1, Gas6, Gsta3, Krt18, Ces1d, Atp1b1, Muc1 
#> 	   Hhex, Acadm, Spp1, Enpp2, Bcl2l14, Sat1, Smtnl2, 1700011H14Rik, Tgm2, Fam159a 
#> StandardPC_ 4 
#> Positive:  Glud1, Tm4sf4, Akr1c19, Cldn4, Runx1t1, Fev, Pou3f4, Gm43861, Pgrmc1, Arx 
#> 	   Cd200, Lrpprc, Hmgn3, Ppp1r14c, Pam, Etv1, Tsc22d1, Slc25a5, Akap17b, Pgf 
#> 	   Fam43a, Emb, Jun, Krt8, Dnajc12, Mid1ip1, Ids, Rgs17, Uchl1, Alcam 
#> Negative:  Ins2, Ins1, Ppp1r1a, Nnat, Calr, Sytl4, Sdf2l1, Iapp, Pdia6, Mapt 
#> 	   G6pc2, C2cd4b, Npy, Gng12, P2ry1, Ero1lb, Adra2a, Papss2, Arhgap36, Fam151a 
#> 	   Dlk1, Creld2, Gip, Tmem215, Gm27033, Cntfr, Prss53, C2cd4a, Lyve1, Ociad2 
#> StandardPC_ 5 
#> Positive:  Pdx1, Nkx6-1, Npepl1, Cldn4, Cryba2, Fev, Jun, Chgb, Gng12, Adra2a 
#> 	   Mnx1, Sytl4, Pdk3, Gm27033, Nnat, Chga, Ins2, 1110012L19Rik, Enho, Krt7 
#> 	   Mlxipl, Tmsb10, Flrt1, Pax4, Tubb3, Prrg2, Gars, Frzb, BC023829, Gm2694 
#> Negative:  Irx2, Irx1, Gcg, Ctxn2, Tmem27, Ctsz, Tmsb15l, Nap1l5, Pou6f2, Gria2 
#> 	   Ghrl, Peg10, Smarca1, Arx, Lrpap1, Rgs4, Ttr, Gast, Tmsb15b2, Serpina1b 
#> 	   Slc16a10, Wnk3, Ly6e, Auts2, Sct, Arg1, Dusp10, Sphkap, Dock11, Edn3 
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group_by = "CellType"
)
#> Warning: The `slot` argument of `Assays()` is deprecated as of SeuratObject 5.0.0.
#> ℹ Please use `LayerData()` instead.
#> ℹ The deprecated feature was likely used in the scop package.
#>   Please report the issue at <https://github.com/mengxu98/scop/issues>.
#> ⠙ [2025-12-05 08:30:54] Running [1/5] Processing: Ductal  ETA:  1s
#> ✔ [2025-12-05 08:30:54] Completed 5 tasks in 871ms
#> 
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$gene,
  group.by = "CellType",
  split.by = "Phase",
  cell_split_palette = "Dark2"
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$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$message = FALSE` to turn off this message.
ht1$plot


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


ht2 <- FeatureHeatmap(
  pancreas_sub,
  features = de_filter$gene,
  group.by = c("CellType", "SubCellType"),
  n_split = 4,
  cluster_rows = TRUE,
  cluster_row_slices = TRUE,
  cluster_columns = TRUE,
  cluster_column_slices = TRUE,
  ht_params = list(row_gap = grid::unit(0, "mm")),
  use_raster = FALSE
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.

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
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
#>  
#> → Will install 51 packages.
#> → All 51 packages (0 B) are cached.
#> + AnnotationDbi       1.72.0  [bld]
#> + AnnotationHub       4.0.0   [bld][cmp]
#> + BiocBaseUtils       1.12.0  [bld]
#> + BiocFileCache       3.0.0   [bld]
#> + BiocVersion         3.22.0  [bld]
#> + Biostrings          2.78.0  [bld][cmp]
#> + DBI                 1.2.3   
#> + DOSE                4.4.0   [bld]
#> + GO.db               3.22.0  [bld]
#> + GOSemSim            2.36.0  [bld][cmp]
#> + KEGGREST            1.50.0  [bld]
#> + R.methodsS3         1.8.2   
#> + R.oo                1.27.1  
#> + R.utils             2.13.0  
#> + RSQLite             2.4.5   
#> + ape                 5.8-1   
#> + bit                 4.6.0   
#> + bit64               4.6.0-1 
#> + blob                1.2.4   
#> + clipr               0.8.0    + ✔ libx11-dev
#> + clusterProfiler     4.18.2  [bld]
#> + dbplyr              2.5.1   
#> + enrichplot          1.30.4  [bld]
#> + fastmatch           1.1-6   
#> + fgsea               1.36.0  [bld][cmp]
#> + filelock            1.0.3   
#> + fontBitstreamVera   0.1.1   
#> + fontLiberation      0.1.0   
#> + fontquiver          0.2.1   
#> + gdtools             0.4.4    + ✔ libcairo2-dev, ✔ libfontconfig1-dev, ✔ libfreetype6-dev
#> + ggforce             0.5.0   
#> + ggiraph             0.9.2    + ✔ libpng-dev
#> + ggnewscale          0.5.2   
#> + ggtangle            0.0.9   
#> + ggtree              4.0.1   [bld]
#> + gson                0.1.0   
#> + hms                 1.1.4   
#> + httr2               1.2.1   
#> + org.Hs.eg.db        3.22.0  [bld]
#> + quarto              1.5.1   
#> + qvalue              2.42.0  [bld]
#> + readr               2.1.6   
#> + rstudioapi          0.17.1  
#> + scatterpie          0.2.6   
#> + systemfonts         1.3.1    + ✔ libfontconfig1-dev, ✔ libfreetype6-dev
#> + tidydr              0.0.6   
#> + tidytree            0.4.6   
#> + treeio              1.34.0  [bld]
#> + tweenr              2.0.3   
#> + tzdb                0.5.0   
#> + vroom               1.6.7   
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 51 pkgs are cached
#> ✔ Got BiocVersion 3.22.0 (source) (1.11 kB)
#> ✔ Got blob 1.2.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (47.47 kB)
#> ✔ Got BiocBaseUtils 1.12.0 (source) (232.56 kB)
#> ✔ Got clipr 0.8.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (51.24 kB)
#> ✔ Got filelock 1.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (24.70 kB)
#> ✔ Got bit64 4.6.0-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (492.54 kB)
#> ✔ Got BiocFileCache 3.0.0 (source) (744.19 kB)
#> ✔ Got bit 4.6.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (628.10 kB)
#> ✔ Got ggtangle 0.0.9 (x86_64-pc-linux-gnu-ubuntu-24.04) (257.09 kB)
#> ✔ Got clusterProfiler 4.18.2 (source) (632.38 kB)
#> ✔ Got AnnotationHub 4.0.0 (source) (1.00 MB)
#> ✔ Got scatterpie 0.2.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (150.90 kB)
#> ✔ Got dbplyr 2.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.24 MB)
#> ✔ Got RSQLite 2.4.5 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.35 MB)
#> ✔ Got tzdb 0.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (666.60 kB)
#> ✔ Got GOSemSim 2.36.0 (source) (610.99 kB)
#> ✔ Got fontBitstreamVera 0.1.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (699.47 kB)
#> ✔ Got hms 1.1.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (103.38 kB)
#> ✔ Got fastmatch 1.1-6 (x86_64-pc-linux-gnu-ubuntu-24.04) (35.95 kB)
#> ✔ Got gdtools 0.4.4 (x86_64-pc-linux-gnu-ubuntu-24.04) (203.79 kB)
#> ✔ Got rstudioapi 0.17.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (317.69 kB)
#> ✔ Got ggtree 4.0.1 (source) (370.24 kB)
#> ✔ Got gson 0.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (232.54 kB)
#> ✔ Got KEGGREST 1.50.0 (source) (239.73 kB)
#> ✔ Got qvalue 2.42.0 (source) (2.77 MB)
#> ✔ Got ape 5.8-1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.97 MB)
#> ✔ Got vroom 1.6.7 (x86_64-pc-linux-gnu-ubuntu-24.04) (966.05 kB)
#> ✔ Got fontquiver 0.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (2.28 MB)
#> ✔ Got R.methodsS3 1.8.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (82.67 kB)
#> ✔ Got tweenr 2.0.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (461.68 kB)
#> ✔ Got treeio 1.34.0 (source) (701.64 kB)
#> ✔ Got readr 2.1.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (868.61 kB)
#> ✔ Got ggiraph 0.9.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.67 MB)
#> ✔ Got ggforce 0.5.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.95 MB)
#> ✔ Got tidytree 0.4.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (343.02 kB)
#> ✔ Got R.oo 1.27.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (996.09 kB)
#> ✔ Got quarto 1.5.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (544.37 kB)
#> ✔ Got ggnewscale 0.5.2 (x86_64-pc-linux-gnu-ubuntu-24.04) (351.15 kB)
#> ✔ Got DBI 1.2.3 (x86_64-pc-linux-gnu-ubuntu-24.04) (916.93 kB)
#> ✔ Got systemfonts 1.3.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (816.45 kB)
#> ✔ Got AnnotationDbi 1.72.0 (source) (4.38 MB)
#> ✔ Got httr2 1.2.1 (x86_64-pc-linux-gnu-ubuntu-24.04) (782.87 kB)
#> ✔ Got DOSE 4.4.0 (source) (5.75 MB)
#> ✔ Got R.utils 2.13.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (1.45 MB)
#> ✔ Got fgsea 1.36.0 (source) (6.17 MB)
#> ✔ Got fontLiberation 0.1.0 (x86_64-pc-linux-gnu-ubuntu-24.04) (4.54 MB)
#> ✔ Got Biostrings 2.78.0 (source) (12.82 MB)
#> ✔ Got GO.db 3.22.0 (source) (25.25 MB)
#> ✔ Got org.Hs.eg.db 3.22.0 (source) (104.97 MB)
#> ℹ Installing system requirements
#> ℹ Executing `sudo sh -c apt-get -y update`
#> Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [144 B]
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu noble InRelease
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:3 http://azure.archive.ubuntu.com/ubuntu noble-updates InRelease
#> Hit:4 http://azure.archive.ubuntu.com/ubuntu noble-backports InRelease
#> Hit:5 http://azure.archive.ubuntu.com/ubuntu noble-security InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install libx11-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libpng-dev libcurl4-openssl-dev libssl-dev make libglpk-dev libxml2-dev pandoc libicu-dev`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libx11-dev is already the newest version (2:1.8.7-1build1).
#> libx11-dev set to manually installed.
#> libcairo2-dev is already the newest version (1.18.0-3build1).
#> libfontconfig1-dev is already the newest version (2.15.0-1.1ubuntu2).
#> libfreetype-dev is already the newest version (2.13.2+dfsg-1build3).
#> libpng-dev is already the newest version (1.6.43-5build1).
#> libcurl4-openssl-dev is already the newest version (8.5.0-2ubuntu10.6).
#> libssl-dev is already the newest version (3.0.13-0ubuntu3.6).
#> make is already the newest version (4.3-4.1build2).
#> libglpk-dev is already the newest version (5.0-1build2).
#> libxml2-dev is already the newest version (2.9.14+dfsg-1.3ubuntu3.6).
#> pandoc is already the newest version (3.1.3+ds-2).
#> libicu-dev is already the newest version (74.2-1ubuntu3.1).
#> 0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
#> ℹ Building BiocBaseUtils 1.12.0
#> ℹ Building BiocVersion 3.22.0
#> ℹ Building Biostrings 2.78.0
#> ℹ Building qvalue 2.42.0
#> ✔ Built BiocVersion 3.22.0 (1.5s)
#> ✔ Installed ape 5.8-1  (103ms)
#> ✔ Installed bit 4.6.0  (42ms)
#> ✔ Installed bit64 4.6.0-1  (1.1s)
#> ✔ Built BiocBaseUtils 1.12.0 (3.2s)
#> ✔ Installed blob 1.2.4  (117ms)
#> ✔ Installed clipr 0.8.0  (163ms)
#> ✔ Installed DBI 1.2.3  (135ms)
#> ✔ Installed dbplyr 2.5.1  (134ms)
#> ✔ Installed fastmatch 1.1-6  (113ms)
#> ℹ Building fgsea 1.36.0
#> ✔ Installed filelock 1.0.3  (203ms)
#> ✔ Installed fontBitstreamVera 0.1.1  (53ms)
#> ✔ Installed fontLiberation 0.1.0  (94ms)
#> ✔ Installed fontquiver 0.2.1  (1.1s)
#> ✔ Installed gdtools 0.4.4  (121ms)
#> ✔ Built qvalue 2.42.0 (5.4s)
#> ✔ Installed ggforce 0.5.0  (110ms)
#> ✔ Installed ggiraph 0.9.2  (131ms)
#> ✔ Installed ggnewscale 0.5.2  (118ms)
#> ✔ Installed ggtangle 0.0.9  (114ms)
#> ✔ Installed gson 0.1.0  (126ms)
#> ✔ Installed hms 1.1.4  (146ms)
#> ✔ Installed httr2 1.2.1  (232ms)
#> ✔ Installed quarto 1.5.1  (149ms)
#> ✔ Installed R.methodsS3 1.8.2  (138ms)
#> ✔ Installed R.oo 1.27.1  (137ms)
#> ✔ Installed R.utils 2.13.0  (130ms)
#> ✔ Installed readr 2.1.6  (139ms)
#> ✔ Installed RSQLite 2.4.5  (161ms)
#> ℹ Building BiocFileCache 3.0.0
#> ✔ Installed rstudioapi 0.17.1  (231ms)
#> ✔ Installed scatterpie 0.2.6  (59ms)
#> ✔ Installed systemfonts 1.3.1  (55ms)
#> ✔ Installed tidydr 0.0.6  (62ms)
#> ✔ Installed tidytree 0.4.6  (36ms)
#> ℹ Building treeio 1.34.0
#> ✔ Built BiocFileCache 3.0.0 (8.4s)
#> ✔ Installed tweenr 2.0.3  (75ms)
#> ✔ Installed tzdb 0.5.0  (102ms)
#> ✔ Installed vroom 1.6.7  (120ms)
#> ✔ Installed BiocBaseUtils 1.12.0  (91ms)
#> ✔ Installed BiocFileCache 3.0.0  (58ms)
#> ✔ Installed BiocVersion 3.22.0  (51ms)
#> ✔ Installed qvalue 2.42.0  (125ms)
#> ✔ Built treeio 1.34.0 (9.4s)
#> ✔ Installed treeio 1.34.0  (63ms)
#> ℹ Building ggtree 4.0.1
#> ✔ Built ggtree 4.0.1 (12s)
#> ✔ Installed ggtree 4.0.1  (111ms)
#> ✔ Built Biostrings 2.78.0 (32.4s)
#> ✔ Installed Biostrings 2.78.0  (170ms)
#> ℹ Building KEGGREST 1.50.0
#> ✔ Built fgsea 1.36.0 (33.1s)
#> ✔ Installed fgsea 1.36.0  (132ms)
#> ✔ Built KEGGREST 1.50.0 (5s)
#> ✔ Installed KEGGREST 1.50.0  (26ms)
#> ℹ Building AnnotationDbi 1.72.0
#> ✔ Built AnnotationDbi 1.72.0 (11.6s)
#> ✔ Installed AnnotationDbi 1.72.0  (70ms)
#> ℹ Building AnnotationHub 4.0.0
#> ℹ Building GO.db 3.22.0
#> ℹ Building org.Hs.eg.db 3.22.0
#> ✔ Built AnnotationHub 4.0.0 (12.3s)
#> ✔ Installed AnnotationHub 4.0.0  (58ms)
#> ✔ Built GO.db 3.22.0 (37.4s)
#> ✔ Installed GO.db 3.22.0  (490ms)
#> ℹ Building GOSemSim 2.36.0
#> ✔ Built GOSemSim 2.36.0 (13.2s)
#> ✔ Installed GOSemSim 2.36.0  (41ms)
#> ℹ Building DOSE 4.4.0
#> ✔ Built DOSE 4.4.0 (11.6s)
#> ✔ Installed DOSE 4.4.0  (55ms)
#> ℹ Building enrichplot 1.30.4
#> ✔ Built enrichplot 1.30.4 (11.5s)
#> ✔ Installed enrichplot 1.30.4  (23ms)
#> ℹ Building clusterProfiler 4.18.2
#> ✔ Built clusterProfiler 4.18.2 (12.3s)
#> ✔ Installed clusterProfiler 4.18.2  (31ms)
#> ✔ Built org.Hs.eg.db 3.22.0 (3m 56.2s)
#> ✔ Installed org.Hs.eg.db 3.22.0  (2.1s)
#> ✔ 1 pkg + 155 deps: kept 105, added 51, dld 49 (195.15 MB) [5m 13.9s]
#> Error in loadNamespace(x): there is no package called ‘R.cache’
ht3$plot
#> Error: object 'ht3' not found

pancreas_sub <- RunSlingshot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP"
)
#> Error in loadNamespace(x): there is no package called ‘slingshot’
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("Paired", "cividis")
)
#> Error in 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("Paired", "cividis")): Cell_annotation: Lineage1 is not in the Seurat object.
ht4$plot
#> Error: object 'ht4' not found

if (FALSE) { # \dontrun{
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
} # }