This function 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,
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 = 0.5,
palette = "Spectral",
palcolor = NULL,
aspect.ratio = 1,
legend.position = "right",
legend.direction = "vertical",
theme_use = "theme_scp",
theme_args = list(),
combine = TRUE,
nrow = NULL,
ncol = NULL,
byrow = TRUE,
seed = 11
)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
resarguments must be provided.- db
The database to use for enrichment plot. Default is "GO_BP".
- group_by
A character vector specifying the grouping variable in the Seurat object. This argument is only used if
srtis specified.- test.use
A character vector specifying the test to be used in differential expression analysis. This argument is only used if
srtis 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". Default is "bar".
- 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. Default is "Database".
- group_use
The group(s) to be used for enrichment plot. Default is NULL.
- 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. Default is NULL. Only work when
padjustCutoffis NULL.- padjustCutoff
The p-adjusted cutoff. Default is 0.05.
- 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. Default is FALSE.
- topWord
The number of top words to display for wordcloud. Default is 100.
- word_type
The type of words to display in wordcloud. Options are "term" and "feature". Default is "term".
- word_size
The size range for words in wordcloud. Default is c(2, 8).
- words_excluded
Words to be excluded from the wordcloud. The default value is NULL, which means that the built-in words (SCP::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. Default is "fr".
- network_labelsize
The label size for network plot. Default is 5.
- network_blendmode
The blend mode for network plot. Default is "blend".
- network_layoutadjust
Whether to adjust the layout of the network plot to avoid overlapping words. Default is TRUE.
- network_adjscale
The scale for adjusting network plot layout. Default is 60.
- network_adjiter
The number of iterations for adjusting network plot layout. Default is 100.
- enrichmap_layout
The layout algorithm to use for enrichmap plot. Options are "fr", "kk","random", "circle", "tree", "grid", or other algorithm from 'igraph' package. Default is "fr".
- enrichmap_cluster
The clustering algorithm to use for enrichmap plot. Options are "walktrap", "fast_greedy", or other algorithm from 'igraph' package. Default is "fast_greedy".
- enrichmap_label
The label type for enrichmap plot. Options are "term" and "feature". Default is "term".
- enrichmap_labelsize
The label size for enrichmap plot. Default is 5.
- enrlichmap_nlabel
The number of labels to display for each cluster in enrichmap plot. Default is 4.
- enrichmap_show_keyword
Whether to show the keyword of terms or features in enrichmap plot. Default is FALSE.
- enrichmap_mark
The mark shape for enrichmap plot. Options are "ellipse" and "hull". Default is "ellipse".
- enrichmap_expand
The expansion factor for enrichmap plot. Default is c(0.5, 0.5).
- character_width
The maximum width of character of descriptions. Default is 50.
- lineheight
The line height for y-axis labels. Default is 0.5.
- palette
The color palette to use. Default is "Spectral".
- palcolor
Custom colors for palette. Default is NULL.
- aspect.ratio
The aspect ratio of the plot. Default is 1.
- legend.position
The position of the legend. Default is "right".
- legend.direction
The direction of the legend. Default is "vertical".
- theme_use
The theme to use for the plot. Default is "theme_scp".
- theme_args
The arguments to pass to the theme. Default is an empty list.
- combine
Whether to combine multiple plots into a single plot. Default is TRUE.
- nrow
The number of rows in the combined plot. Default is NULL, calculated based on the number of plots.
- ncol
The number of columns in the combined plot. Default is NULL, calculated based on the number of plots.
- byrow
Whether to fill the combined plot by row. Default is TRUE.
- seed
The random seed to use. Default is 11.
Examples
data("pancreas_sub")
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 07:13:19.485699] Start DEtest
#> Workers: 2
#> Find all markers(wilcox) among 5 groups...
#>
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#> [2023-11-21 07:13:30.012413] DEtest done
#> Elapsed time:10.53 secs
pancreas_sub <- RunEnrichment(srt = pancreas_sub, db = c("GO_BP", "GO_CC"), group_by = "CellType", species = "Mus_musculus")
#> [2023-11-21 07:13:30.016153] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: GO_BP version:3.17.0 nterm:16027 created:2023-11-21 07:12:49.800522
#> Preparing database: GO_BP
#> Preparing database: GO_CC
#> 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?
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "bar")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "bar"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub,
db = "GO_BP", group_by = "CellType", group_use = "Endocrine",
plot_type = "bar", character_width = 30,
theme_use = ggplot2::theme_classic, theme_args = list(base_size = 10)
)
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Endocrine", plot_type = "bar", character_width = 30, theme_use = ggplot2::theme_classic, theme_args = list(base_size = 10)): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", plot_type = "bar", color_by = "Groups", ncol = 2)
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", plot_type = "bar", color_by = "Groups", ncol = 2): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub,
db = "GO_BP", group_by = "CellType", plot_type = "bar",
split_by = "Database", color_by = "Groups", palette = "Set1",
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"),
"Endocrine" = c("GO:0009914", "GO:0030073", "GO:0009743", "GO:0042593")
)
)
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", plot_type = "bar", split_by = "Database", color_by = "Groups", palette = "Set1", 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"), Endocrine = c("GO:0009914", "GO:0030073", "GO:0009743", "GO:0042593"))): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", topTerm = 3, plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", topTerm = 3, plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", topTerm = 3, plot_type = "comparison", compare_only_sig = TRUE)
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", topTerm = 3, plot_type = "comparison", compare_only_sig = TRUE): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = c("Ductal", "Endocrine"), plot_type = "comparison")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = c("Ductal", "Endocrine"), plot_type = "comparison"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub,
db = c("GO_BP", "GO_CC"), group_by = "CellType", group_use = c("Ductal", "Endocrine"), plot_type = "bar",
split_by = "Groups"
)
#> Error in EnrichmentPlot(pancreas_sub, db = c("GO_BP", "GO_CC"), group_by = "CellType", group_use = c("Ductal", "Endocrine"), plot_type = "bar", split_by = "Groups"): No enrichment result found. You may perform RunEnrichment first.
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",
)
#> Error in 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", ): No enrichment result found. You may perform RunEnrichment first.
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")
)
#> Error in 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")): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub,
db = c("GO_BP", "GO_CC"), group_by = "CellType", group_use = c("Ductal", "Endocrine"), plot_type = "bar",
split_by = c("Groups", "Database")
)
#> Error in EnrichmentPlot(pancreas_sub, db = c("GO_BP", "GO_CC"), group_by = "CellType", group_use = c("Ductal", "Endocrine"), plot_type = "bar", split_by = c("Groups", "Database")): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub,
db = c("GO_BP", "GO_CC"), group_by = "CellType", plot_type = "bar",
split_by = "Database", color_by = "Groups", palette = "Set1"
)
#> Error in EnrichmentPlot(pancreas_sub, db = c("GO_BP", "GO_CC"), group_by = "CellType", plot_type = "bar", split_by = "Database", color_by = "Groups", palette = "Set1"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "dot", palette = "GdRd")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "dot", palette = "GdRd"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "lollipop", palette = "GdRd")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "lollipop", palette = "GdRd"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "wordcloud")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "wordcloud"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "wordcloud", word_type = "feature")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "wordcloud", word_type = "feature"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "network")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "network"): No enrichment result found. You may perform RunEnrichment first.
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"))
#> Error in 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")): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "network", network_layoutadjust = FALSE)
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "network", network_layoutadjust = FALSE): No enrichment result found. You may perform RunEnrichment first.
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)
) %>% panel_fix(height = 5)
#> Error in 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)): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "enrichmap")
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "enrichmap"): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "enrichmap", enrichmap_expand = c(2, 1))
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "enrichmap", enrichmap_expand = c(2, 1)): No enrichment result found. You may perform RunEnrichment first.
EnrichmentPlot(pancreas_sub,
db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "enrichmap",
enrichmap_show_keyword = TRUE, character_width = 10
)
#> Error in EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "enrichmap", enrichmap_show_keyword = TRUE, character_width = 10): No enrichment result found. You may perform RunEnrichment first.
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)
) %>% panel_fix(height = 4)
#> Error in 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)): No enrichment result found. You may perform RunEnrichment first.
pancreas_sub <- RunEnrichment(srt = pancreas_sub, db = c("MP", "DO"), group_by = "CellType", convert_species = TRUE, species = "Mus_musculus")
#> [2023-11-21 07:14:27.071083] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Preparing database: MP
#> Preparing database: DO
#> Permform enrichment...
#>
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#>
#> [2023-11-21 07:14:51.88477] Enrichment done
#> Elapsed time:24.81 secs
EnrichmentPlot(pancreas_sub, db = c("MP", "DO"), group_by = "CellType", group_use = "Endocrine", ncol = 1)
