EnrichmentPlot: EnrichmentPlot
In zh542370159/SCP: Single Cell Pipeline
EnrichmentPlot R Documentation
EnrichmentPlot
Description
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 res arguments 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 srt is specified.
test.use
A character vector specifying the 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". 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 padjustCutoff is 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.
See Also
RunEnrichment
Examples
data("pancreas_sub")
pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType")
pancreas_sub <- RunEnrichment(srt = pancreas_sub, db = c("GO_BP", "GO_CC"), group_by = "CellType", species = "Mus_musculus")
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "bar")
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)
)
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",
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")
)
)
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", group_use = c("Ductal", "Endocrine"), plot_type = "bar",
split_by = c("Groups", "Database")
)
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")
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"))
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "network", network_layoutadjust = FALSE)
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)
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)
) %>% panel_fix(height = 4)
pancreas_sub <- RunEnrichment(srt = pancreas_sub, db = c("MP", "DO"), group_by = "CellType", convert_species = TRUE, species = "Mus_musculus")
EnrichmentPlot(pancreas_sub, db = c("MP", "DO"), group_by = "CellType", group_use = "Endocrine", ncol = 1)
zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.
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| EnrichmentPlot | R Documentation |
EnrichmentPlot
Description
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 |
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 |
test.use |
A character vector specifying the test to be used in differential expression analysis. This argument is only used if |
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 |
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. |
See Also
RunEnrichment
Examples
data("pancreas_sub")
pancreas_sub <- RunDEtest(pancreas_sub, group_by = "CellType")
pancreas_sub <- RunEnrichment(srt = pancreas_sub, db = c("GO_BP", "GO_CC"), group_by = "CellType", species = "Mus_musculus")
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "bar")
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)
)
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",
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")
)
)
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", group_use = c("Ductal", "Endocrine"), plot_type = "bar",
split_by = c("Groups", "Database")
)
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")
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"))
EnrichmentPlot(pancreas_sub, db = "GO_BP", group_by = "CellType", group_use = "Ductal", plot_type = "network", network_layoutadjust = FALSE)
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)
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)
) %>% panel_fix(height = 4)
pancreas_sub <- RunEnrichment(srt = pancreas_sub, db = c("MP", "DO"), group_by = "CellType", convert_species = TRUE, species = "Mus_musculus")
EnrichmentPlot(pancreas_sub, db = c("MP", "DO"), group_by = "CellType", group_use = "Endocrine", ncol = 1)
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