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Ferris Wheel Plot

Source: R/FerrisWheelPlot.R
FerrisWheelPlot.Rd

Draw a Ferris wheel-style donut plot for up/down counts across pathways or other categories. The center donut shows the total counts, and outer donuts show category-level counts with radius scaled by category size.

Usage

FerrisWheelPlot(
  data = NULL,
  res = NULL,
  label_col = "pathway",
  up_col = "up",
  down_col = "down",
  total_up = NULL,
  total_down = NULL,
  de_results = NULL,
  term_col = "Description",
  group_col = "Groups",
  count_col = "Count",
  padj_col = "p.adjust",
  up_group = "Up",
  down_group = "Down",
  padj_cutoff = 0.05,
  top_n = 10,
  up_label = "Up-regulated Genes",
  down_label = "Down-regulated Genes",
  up_color = NULL,
  down_color = NULL,
  palette = "Chinese",
  palcolor = NULL,
  center_label = "Significant Genes",
  center_radius = 1.25,
  center_width = 0.28,
  outer_distance = 2.55,
  outer_width = 0.12,
  min_outer_radius = 0.28,
  max_outer_radius = 0.48,
  label_wrap = 26,
  label_case = c("title", "none"),
  label.stroke = 0.2,
  label.stroke.color = "white",
  label.size = 3,
  number.size = 3,
  center.size = 4.5,
  legend.size = 3.5,
  line.color = "grey35",
  line.linewidth = 0.35,
  legend.position = c("bottom", "none"),
  direction = 1,
  start = pi/2,
  theme_use = "theme_scop",
  theme_args = list()
)

Arguments

data

A data.frame containing category labels and two non-negative count columns. If NULL, the table is built from res.

res

A result list returned by RunEnrichment() or an enrichment data.frame. When provided, FerrisWheelPlot() summarizes enriched terms into up/down counts internally.

label_col

Column name for category labels. Default is "pathway".

up_col

Column name for up-regulated counts. Default is "up".

down_col

Column name for down-regulated counts. Default is "down".

total_up, total_down

Total counts shown in the center donut. When NULL, the corresponding column sum is used. For enrichment input, these can be inferred from de_results.

de_results

Optional differential expression result table used to infer total_up and total_down from avg_log2FC.

term_col, group_col, count_col, padj_col

Column names used when res is an enrichment result. Defaults match RunEnrichment() output.

up_group, down_group

Group labels in enrichment results. Default matches examples that use "Up" and "Down" as geneID_groups.

padj_cutoff

Adjusted p-value cutoff used to select enriched terms from res.

top_n

Number of enriched terms to show when res is provided. Default is 10.

up_label, down_label

Legend labels and center text labels. Defaults are "Up-regulated Genes" and "Down-regulated Genes".

up_color, down_color

Optional colors for up/down counts. When NULL, colors are selected from the "Chinese" palette used by scop.

palette, palcolor

Palette passed to thisplot::palette_colors() when up_color or down_color is not provided.

center_label

Text shown inside the center donut. Default is "Significant Genes".

center_radius

Radius of the center donut. Default is 1.25.

center_width

Width of the center donut band. Default is 0.28.

outer_distance

Distance from plot center to outer donut centers. Default is 2.55.

outer_width

Width of outer donut bands. Default is 0.12.

min_outer_radius, max_outer_radius

Minimum and maximum outer donut radii after scaling by category count.

label_wrap

Maximum characters per category label line. Set NULL to disable wrapping.

label_case

Label case for category names. "title" capitalizes words by default; "none" keeps labels unchanged.

label.stroke

White outline width around text labels. Default is 0.1. Set 0 to disable the outline.

label.stroke.color

Outline color for text labels.

label.size, number.size, center.size, legend.size

Text sizes.

line.color, line.linewidth

Connector line styling.

legend.position

Position of the compact legend. Use "bottom" or "none".

direction

Drawing direction for the outer donuts. 1 is clockwise and -1 is counterclockwise.

start

Start angle in radians for the first category. Default is pi / 2.

theme_use

Theme function name. Default is "theme_scop".

theme_args

Additional arguments passed to theme_use.

Value

A ggplot object.

See also

EnrichmentPlot, DEtestPlot

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunDEtest(
  pancreas_sub,
  group.by = "CellType",
  only.pos = FALSE
)

de_df <- pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox
de_df <- de_df[
  de_df$p_val_adj < 0.05 & abs(de_df$avg_log2FC) > 0.25,
  ,
  drop = FALSE
]
de_df$direction <- ifelse(de_df$avg_log2FC > 0, "Up", "Down")

enrich_out <- RunEnrichment(
  geneID = de_df$gene,
  geneID_groups = de_df$direction,
  db = "GO_BP",
  species = "Mus_musculus"
)
FerrisWheelPlot(
  res = enrich_out,
  de_results = de_df
)