Enrichment Plot

Generates various types of plots for enrichment (over-representation) analysis.

Usage

EnrichmentPlot(
  object = NULL,
  db = "GO_BP",
  group.by = NULL,
  test.use = "wilcox",
  res = NULL,
  plot_type = c("bar", "dot", "lollipop", "network", "enrichmap", "wordcloud",
    "comparison"),
  split_by = c("Database", "Groups"),
  color_by = "Database",
  group_use = NULL,
  id_use = NULL,
  pvalueCutoff = NULL,
  padjustCutoff = 0.05,
  score_col = NULL,
  scoreCutoff = NULL,
  score_label = "Score",
  topTerm = ifelse(plot_type == "enrichmap", 100, 6),
  compare_only_sig = FALSE,
  topWord = 100,
  word_type = c("term", "feature"),
  word_size = c(2, 8),
  words_excluded = NULL,
  network_layout = "fr",
  network_labelsize = 5,
  network_blendmode = "blend",
  network_layoutadjust = TRUE,
  network_adjscale = 60,
  network_adjiter = 100,
  enrichmap_layout = "fr",
  enrichmap_cluster = "fast_greedy",
  enrichmap_label = c("term", "feature"),
  enrichmap_labelsize = 5,
  enrichmap_nlabel = 4,
  enrlichmap_nlabel = NULL,
  enrichmap_show_keyword = FALSE,
  enrichmap_mark = c("ellipse", "hull"),
  enrichmap_expand = c(0.5, 0.5),
  character_width = 50,
  lineheight = 0.7,
  palette = "Spectral",
  palcolor = NULL,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 11,
  verbose = TRUE,
  srt = NULL
)

Arguments

object: A Seurat object containing the results of RunDEtest and RunEnrichment. If specified, enrichment results will be extracted from the Seurat object automatically. If not specified, the res arguments must be provided.
db: The database to use for enrichment plot.
group.by: Grouping variable in the Seurat object. This argument is only used if object is specified. NULL (the default) selects the results that RunEnrichment stored for custom gene sets or custom cell groups, which are keyed as "custom".
test.use: Test to be used in differential expression analysis. This argument is only used if object is specified.
res: Enrichment results generated by RunEnrichment function. If provided, 'object', 'test.use' and 'group.by' are ignored.
plot_type: The type of plot to generate. Options are: "bar", "dot", "lollipop", "network", "enrichmap", "wordcloud", "comparison".
split_by: The splitting variable(s) for the plot. Can be "Database", "Groups", or both. Default is c("Database", "Groups") for plots.
color_by: The variable used for coloring.
group_use: The group(s) to be used for enrichment plot.
id_use: List of IDs to be used to display specific terms in the enrichment plot. Default value is NULL.
pvalueCutoff: The p-value cutoff. Only work when padjustCutoff is NULL.
padjustCutoff: The p-adjusted cutoff.
score_col: Optional numeric score column. When supplied, terms are ranked and weighted by the absolute score and no p-value semantics are used. This is intended for activity or importance results such as pathway scores.
scoreCutoff: Optional minimum absolute score used with score_col.
score_label: Legend label used with score_col.
topTerm: The number of top terms to display. Default is 6, or 100 if plot_type is "enrichmap".
compare_only_sig: Whether to compare only significant terms.
topWord: The number of top words to display for wordcloud.
word_type: The type of words to display in wordcloud. Options are "term" and "feature".
word_size: The size range for words in wordcloud.
words_excluded: Words to be excluded from the wordcloud. Default is NULL, which means that the built-in words (words_excluded) will be used.
network_layout: The layout algorithm to use for network plot. Options are "fr", "kk", "random", "circle", "tree", "grid", or other algorithm from igraph package.
network_labelsize: The label size for network plot.
network_blendmode: The blend mode for network plot.
network_layoutadjust: Whether to adjust the layout of the network plot to avoid overlapping words.
network_adjscale: The scale for adjusting network plot layout.
network_adjiter: The number of iterations for adjusting network plot layout.
enrichmap_layout: The layout algorithm to use for enrichmap plot. Options are "fr", "kk", "random", "circle", "tree", "grid", or other algorithm from igraph package.
enrichmap_cluster: The clustering algorithm to use for enrichmap plot. Options are "walktrap", "fast_greedy", or other algorithm from igraph package.
enrichmap_label: The label type for enrichmap plot. Options are "term" and "feature".
enrichmap_labelsize: The label size for enrichmap plot.
enrichmap_nlabel: The number of labels to display for each cluster in enrichmap plot.
enrlichmap_nlabel: Deprecated. Please use enrichmap_nlabel instead.
enrichmap_show_keyword: Whether to show the keyword of terms or features in enrichmap plot.
enrichmap_mark: The mark shape for enrichmap plot. Options are "ellipse" and "hull".
enrichmap_expand: The expansion factor for enrichmap plot.
character_width: The maximum width of character of descriptions.
lineheight: The line height for y-axis labels.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes.
palcolor: Custom colors used to create a color palette.
aspect.ratio: Panel aspect ratio.
legend.position: Legend placement ("none", "left", "right", "bottom", "top"), direction, and title. legend.title = NULL uses the group name.
legend.direction: Legend direction: "horizontal" or "vertical".
theme_use, theme_args: Theme name or function, plus extra theme arguments.
combine, nrow, ncol, byrow: Combine plots with patchwork. combine = FALSE returns a list of ggplots.
seed: Random seed.
verbose: Whether to print messages.
srt: Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-10-11 22:47:40] Start standard processing workflow...
#> ℹ [2026-10-11 22:47:40] Checking a list of <Seurat>...
#> ! [2026-10-11 22:47:40] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-10-11 22:47:40] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 22:47:41] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-10-11 22:47:41] Use the separate HVF from `srt_list`
#> ℹ [2026-10-11 22:47:41] Number of available HVF: 2000
#> ℹ [2026-10-11 22:47:41] Finished check
#> ℹ [2026-10-11 22:47:41] Perform `ScaleData()`
#> ℹ [2026-10-11 22:47:41] Perform pca linear dimension reduction
#> ℹ [2026-10-11 22:47:41] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-10-11 22:47:42] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-10-11 22:47:42] Reorder clusters...
#> ℹ [2026-10-11 22:47:42] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-10-11 22:47:42] Perform umap nonlinear dimension reduction
#> ✔ [2026-10-11 22:47:48] Standard processing workflow completed
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType"
)
#> ℹ [2026-10-11 22:47:48] Data type is log-normalized
#> ℹ [2026-10-11 22:47:48] Start differential expression test
#> ℹ [2026-10-11 22:47:48] Find all markers(wilcox) among [1] 5 groups...
#> ℹ [2026-10-11 22:47:48] Using 1 core
#> ⠙ [2026-10-11 22:47:48] Running for Ductal [1/5] ■■          20% | ETA: 11s
#> ⠹ [2026-10-11 22:47:48] Running for Ngn3-high-EP [2/5] ■■■■        40% | ETA:  …
#> ⠸ [2026-10-11 22:47:48] Running for Endocrine [3/5] ■■■■■■      60% | ETA:  4s
#> ✔ [2026-10-11 22:47:48] Completed 5 tasks in 10.7s
#> 
#> ℹ [2026-10-11 22:47:48] Building results
#> ✔ [2026-10-11 22:47:59] Differential expression test completed

pancreas_sub <- RunEnrichment(
  pancreas_sub,
  db = c("GO_BP", "GO_CC"),
  group.by = "CellType",
  species = "Mus_musculus"
)
#> ℹ [2026-10-11 22:47:59] Start Enrichment analysis
#> ℹ [2026-10-11 22:47:59] Species: "Mus_musculus"
#> ℹ [2026-10-11 22:47:59] Loading cached: GO_BP version: 3.23.0 nterm:14957 created: 2026-10-11 22:40:14
#> ℹ [2026-10-11 22:48:29] Preparing database: GO_BP
#> ℹ [2026-10-11 22:48:39] Preparing database: GO_CC
#> ℹ [2026-10-11 22:48:44] Convert ID types for the GO_BP database
#> ℹ [2026-10-11 22:48:44] Converted ID types using local annotation package org.Mm.eg.db
#> ℹ [2026-10-11 22:48:45] Convert ID types for the GO_CC database
#> ℹ [2026-10-11 22:48:46] Converted ID types using local annotation package org.Mm.eg.db
#> ℹ [2026-10-11 22:48:46] Permform enrichment...
#> ✔ [2026-10-11 22:48:51] Enrichment analysis done

EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "bar"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  plot_type = "bar",
  color_by = "Groups",
  ncol = 2
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  plot_type = "bar",
  id_use = list(
    "Ductal" = c(
      "GO:0002181", "GO:0045787",
      "GO:0006260", "GO:0050679"
    ),
    "Ngn3-low-EP" = c(
      "GO:0050678", "GO:0051101",
      "GO:0072091", "GO:0006631"
    ),
    "Ngn3-high-EP" = c(
      "GO:0035270", "GO:0030325",
      "GO:0008637", "GO:0030856"
    ),
    "Pre-endocrine" = c(
      "GO:0090276", "GO:0031018",
      "GO:0030073", "GO:1903532"
    )
  )
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  topTerm = 3,
  plot_type = "comparison"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  topTerm = 3,
  plot_type = "comparison",
  compare_only_sig = TRUE
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = c("Ductal", "Endocrine"),
  plot_type = "comparison"
)


EnrichmentPlot(
  pancreas_sub,
  db = c("GO_BP", "GO_CC"),
  group.by = "CellType",
  group_use = c("Ductal", "Endocrine"),
  plot_type = "bar",
  split_by = "Groups"
)


EnrichmentPlot(
  pancreas_sub,
  db = c("GO_BP", "GO_CC"),
  group.by = "CellType",
  group_use = c("Ductal", "Endocrine"),
  plot_type = "bar",
  split_by = "Database",
  color_by = "Groups"
)


EnrichmentPlot(
  pancreas_sub,
  db = c("GO_BP", "GO_CC"),
  group.by = "CellType",
  group_use = c("Ductal", "Endocrine"),
  plot_type = "bar",
  split_by = c("Database", "Groups")
)


EnrichmentPlot(
  pancreas_sub,
  db = c("GO_BP", "GO_CC"),
  group.by = "CellType",
  plot_type = "bar",
  split_by = "Database",
  color_by = "Groups",
  palette = "Set1"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "dot",
  palette = "GdRd"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "lollipop",
  palette = "GdRd"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "wordcloud"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "wordcloud",
  word_type = "feature"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "network"
)
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> ◌ [2026-10-11 22:49:11] Installing 1 R packages...
#>  
#> → Package library at /tmp/RtmpZZsmTm/temp_libpath8d3438b020a.
#> → Will install 6 packages.
#> → All 6 packages (0 B) are cached.
#> + fontBitstreamVera   0.1.1 
#> + fontLiberation      0.1.0 
#> + fontquiver          0.2.1 
#> + gdtools             0.5.1  + ✔ libcairo2-dev, ✔ libfontconfig1-dev, ✔ libfreetype6-dev
#> + ggiraph             0.9.6  + ✔ libpng-dev
#> + shadowtext          0.1.6 
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 6 pkgs are cached
#> ✔ Got shadowtext 0.1.6 (x86_64-pc-linux-gnu-ubuntu-24.04) (243.63 kB)
#> 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:6 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:2 http://azure.archive.ubuntu.com/ubuntu 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 libcairo2-dev libfontconfig1-dev libfreetype6-dev libpng-dev cmake make libuv1-dev pandoc`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> libcairo2-dev is already the newest version (1.18.0-3build1).
#> libfontconfig1-dev is already the newest version (2.15.0-1.1ubuntu2).
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#> make is already the newest version (4.3-4.1build2).
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#> pandoc is already the newest version (3.1.3+ds-2).
#> 0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
#> ✔ Installed fontBitstreamVera 0.1.1  (68ms)
#> ✔ Installed fontLiberation 0.1.0  (99ms)
#> ✔ Installed fontquiver 0.2.1  (128ms)
#> ✔ Installed gdtools 0.5.1  (178ms)
#> ✔ Installed ggiraph 0.9.6  (178ms)
#> ✔ Installed shadowtext 0.1.6  (51ms)
#> ✔ 1 pkg + 55 deps: kept 49, added 6, dld 1 (243.63 kB) [4.5s]
#> ✔ [2026-10-11 22:49:16] shadowtext installed successfully


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "network",
  id_use = c(
    "GO:0050678",
    "GO:0035270",
    "GO:0090276",
    "GO:0030073"
  )
)
#> ✔ [2026-10-11 22:49:17] shadowtext installed successfully


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "network",
  network_layoutadjust = FALSE
)
#> ✔ [2026-10-11 22:49:18] shadowtext installed successfully


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "network",
  topTerm = 4,
  network_blendmode = "average",
  theme_use = "theme_blank",
  theme_args = list(add_coord = FALSE)
) |> thisplot::panel_fix(height = 5)
#> ✔ [2026-10-11 22:49:19] shadowtext installed successfully


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "enrichmap"
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "enrichmap",
  enrichmap_expand = c(2, 1)
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "enrichmap",
  enrichmap_show_keyword = TRUE,
  character_width = 10
)


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "enrichmap",
  topTerm = 200,
  enrichmap_mark = "hull",
  enrichmap_label = "feature",
  enrichmap_nlabel = 3,
  character_width = 10,
  theme_use = "theme_blank",
  theme_args = list(add_coord = FALSE)
) |> thisplot::panel_fix(height = 4)


pancreas_sub <- RunEnrichment(
  pancreas_sub,
  db = c("MP", "DO"),
  group.by = "CellType",
  convert_species = TRUE,
  species = "Mus_musculus"
)
#> ℹ [2026-10-11 22:49:23] Start Enrichment analysis
#> ℹ [2026-10-11 22:49:23] Species: "Mus_musculus"
#> ℹ [2026-10-11 22:49:23] Preparing MP database
#> ℹ [2026-10-11 22:49:39] Species: "Mus_musculus"
#> ℹ [2026-10-11 22:49:39] Preparing DO database
#> ℹ [2026-10-11 22:49:44] Permform enrichment...
#> ✔ [2026-10-11 22:49:45] Enrichment analysis done

EnrichmentPlot(
  pancreas_sub,
  db = c("MP", "DO"),
  group.by = "CellType",
  group_use = "Ductal",
  ncol = 1
)

Usage

Arguments

See also

Examples