Enrichment Plot

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 = 0.7,
  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
)

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. Only work when padjustCutoff is NULL. Default 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. 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. 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 0.7.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Spectral".
palcolor: Custom colors used to create a color palette. Default is NULL.
aspect.ratio: Aspect ratio of the panel. Default is 1.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
combine: Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.
nrow: Number of rows in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
ncol: Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.
byrow: Whether to arrange the plots by row in the combined plot. Default is TRUE.
seed: Random seed for reproducibility. Default is 11.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType"
)

pancreas_sub <- RunEnrichment(
  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",
  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"
)

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)
) |> thisplot::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)
) |> thisplot::panel_fix(height = 4)

pancreas_sub <- RunEnrichment(
  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 = "Ductal",
  ncol = 1
)
} # }

Usage

Arguments

See also

Examples