Skip to contents

Enrichment Plot

Source: R/EnrichmentPlot.R
EnrichmentPlot.Rd

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

Usage

EnrichmentPlot(
  srt,
  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,
  enrlichmap_nlabel = 4,
  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
)

Arguments

srt

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 srt is specified.

test.use

Test to be used in differential expression analysis. This argument is only used if srt is specified.

res

Enrichment results generated by RunEnrichment function. If provided, 'srt', '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.

enrlichmap_nlabel

The number of labels to display for each cluster in enrichmap plot.

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.

See also

RunEnrichment

Examples

data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
#> ℹ [2026-08-30 04:24:33] Start standard processing workflow...
#> ℹ [2026-08-30 04:24:33] Checking a list of <Seurat>...
#> ! [2026-08-30 04:24:33] Data 1/1 of the `srt_list` is "unknown"
#> Warning: Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-08-30 04:24:33] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:24:33] Perform `FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-08-30 04:24:33] Use the separate HVF from `srt_list`
#> ℹ [2026-08-30 04:24:33] Number of available HVF: 2000
#> ℹ [2026-08-30 04:24:34] Finished check
#> ℹ [2026-08-30 04:24:34] Perform `ScaleData()`
#> ℹ [2026-08-30 04:24:34] Perform pca linear dimension reduction
#> ℹ [2026-08-30 04:24:34] Use stored estimated dimensions 1:23 for Standardpca
#> ℹ [2026-08-30 04:24:34] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-08-30 04:24:34] Reorder clusters...
#> ℹ [2026-08-30 04:24:34] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-08-30 04:24:34] Perform umap nonlinear dimension reduction
#> ✔ [2026-08-30 04:24:41] Standard processing workflow completed
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType"
)
#> ℹ [2026-08-30 04:24:42] Data type is log-normalized
#> ℹ [2026-08-30 04:24:42] Start differential expression test
#> ℹ [2026-08-30 04:24:42] Find all markers(wilcox) among [1] 5 groups...
#> ✔ [2026-08-30 04:24:42] Differential expression test completed

pancreas_sub <- RunEnrichment(
  pancreas_sub,
  db = c("GO_BP", "GO_CC"),
  group.by = "CellType",
  species = "Mus_musculus"
)
#> ℹ [2026-08-30 04:24:42] Start Enrichment analysis
#> ℹ [2026-08-30 04:24:42] Species: "Mus_musculus"
#> ℹ [2026-08-30 04:24:42] Loading cached: GO_BP version: 3.23.0 nterm:14957 created: 2026-08-30 04:14:47
#> ℹ [2026-08-30 04:25:09] Preparing database: GO_BP
#> ℹ [2026-08-30 04:25:17] Preparing database: GO_CC
#> ℹ [2026-08-30 04:25:21] Convert ID types for the GO_BP database
#> ℹ [2026-08-30 04:25:21] Converted ID types using local annotation package org.Mm.eg.db
#> ℹ [2026-08-30 04:25:23] Convert ID types for the GO_CC database
#> ℹ [2026-08-30 04:25:23] Converted ID types using local annotation package org.Mm.eg.db
#> ℹ [2026-08-30 04:25:24] Permform enrichment...
#> ℹ [2026-08-30 04:25:25] Using 1 core
#> ⠙ [2026-08-30 04:25:25] Running for 1 [1/10] ■           10% | ETA: 13s
#> ⠹ [2026-08-30 04:25:25] Running for 2 [2/10] ■■          20% | ETA: 11s
#> ⠸ [2026-08-30 04:25:25] Running for 4 [4/10] ■■■■        40% | ETA:  9s
#> ⠼ [2026-08-30 04:25:25] Running for 9 [9/10] ■■■■■■■■■   90% | ETA:  1s
#> ✔ [2026-08-30 04:25:25] Completed 10 tasks in 9.2s
#> 
#> ℹ [2026-08-30 04:25:25] Building results
#> ✔ [2026-08-30 04:25:34] 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"
)
#> Warning: One word could not fit on page. It has been removed.


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 'spam'
#> Also defined by ‘BiocGenerics’
#> Found more than one class "dist" in cache; using the first, from namespace 'spam'
#> Also defined by ‘BiocGenerics’
#> ◌ [2026-08-30 04:25:53] Installing 1 R packages...
#>  
#> → Package library at /home/runner/work/_temp/Library.
#> → Will install 1 package.
#> → The package (0 B) is cached.
#> + shadowtext   0.1.6 
#> ✔ All system requirements are already installed.
#>   
#> ℹ No downloads are needed, 1 pkg is 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: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
#> Hit:6 https://packages.microsoft.com/repos/azure-cli noble InRelease
#> Hit:7 https://packages.microsoft.com/ubuntu/24.04/prod noble InRelease
#> Hit:8 https://dl.google.com/linux/chrome-stable/deb stable InRelease
#> Reading package lists...
#> ℹ Executing `sudo sh -c apt-get -y install cmake make libuv1-dev libcairo2-dev libfontconfig1-dev libfreetype6-dev libpng-dev pandoc`
#> Reading package lists...
#> Building dependency tree...
#> Reading state information...
#> cmake is already the newest version (3.28.3-1build7).
#> make is already the newest version (4.3-4.1build2).
#> libuv1-dev is already the newest version (1.48.0-1.1build1).
#> 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-1ubuntu0.1).
#> libpng-dev is already the newest version (1.6.43-5ubuntu0.6).
#> pandoc is already the newest version (3.1.3+ds-2).
#> 0 upgraded, 0 newly installed, 0 to remove and 26 not upgraded.
#> ✔ Installed shadowtext 0.1.6  (1s)
#> ✔ 1 pkg + 55 deps: kept 54, added 1, dld 1 (243.63 kB) [4.7s]
#> ✔ [2026-08-30 04:25:58] 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"
  )
)
#> ✔ [2026-08-30 04:25:59] shadowtext installed successfully


EnrichmentPlot(
  pancreas_sub,
  db = "GO_BP",
  group.by = "CellType",
  group_use = "Ductal",
  plot_type = "network",
  network_layoutadjust = FALSE
)
#> ✔ [2026-08-30 04:25:59] 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)
#> ✔ [2026-08-30 04:26:01] 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",
  enrlichmap_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 [2026-08-30 04:26:04] Start Enrichment analysis
#> ℹ [2026-08-30 04:26:04] Species: "Mus_musculus"
#> ℹ [2026-08-30 04:26:04] Preparing MP database
#> ℹ [2026-08-30 04:26:18] Preparing DO database
#> ℹ [2026-08-30 04:26:22] Permform enrichment...
#> ℹ [2026-08-30 04:26:22] Using 1 core
#> ⠙ [2026-08-30 04:26:22] Running for 1 [1/10] ■           10% | ETA:  3s
#> ✔ [2026-08-30 04:26:22] Completed 10 tasks in 1.9s
#> 
#> ℹ [2026-08-30 04:26:22] Building results
#> ✔ [2026-08-30 04:26:24] Enrichment analysis done

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