ggcluster: Plot KEGG Cluster Visualization
In guokai8/richR: Function Enrichment analysis and Network construction

ggcluster

R Documentation

Plot KEGG Cluster Visualization

Description

This function merges two cluster-plot approaches:

Enrichment mode: requires columns Term, Padj, Significant, Annotated, etc.
GSEA mode: requires columns pathway, padj, NES, etc.

Usage

ggcluster(
  data,
  method = c("auto", "enrich", "gsea"),
  color_low = "pink",
  color_high = "red",
  color_mid = "white",
  size_range = c(0.8, 4),
  curve_color = "grey70",
  curve_size = 0.5,
  vertical_line_color = "darkcyan",
  vertical_line_size = 1.5,
  dot_line_color = "grey70",
  dot_line_size = 0.3,
  dot_line_type = "dotted",
  vline_color = "grey80",
  vline_type = "dashed",
  label_font_size = 3,
  label_font_face = "bold",
  pathway_font_size = 2.5,
  pathway_font_face = "italic",
  legend_position = "right",
  x_pathway_offset = 0.3,
  label_x_size = 6,
  plot_margins = c(5, 200, 10, 250),
  ...
)

Arguments

`data`	A data frame containing KEGG cluster data. Must include columns: 'Term', 'Level2', 'group', 'Padj', 'Significant', and 'Annotated'.
`method`	One of `"enrich"` or `"gsea"`. If `"auto"`, guessed from columns.
`color_low`	Color for the lowest value in the gradient (default: "pink").
`color_high`	Color for the highest value in the gradient (default: "red").
`color_mid`	Color for the middle value in the gradient (default: "white").
`size_range`	A numeric vector of length 2 to control the size range of points (default: c(0.8, 4)).
`curve_color`	Color for the connecting curves between Level2 and Terms (default: "grey70").
`curve_size`	Line width for the connecting curves (default: 0.5).
`vertical_line_color`	Color for the vertical lines between Level2 labels and Terms (default: "darkcyan").
`vertical_line_size`	Width of vertical lines between Level2 and Terms (default: 1.5).
`dot_line_color`	Color for dotted lines connecting clusters to pathways (default: "grey70").
`dot_line_size`	Line width for the dotted lines (default: 0.3).
`dot_line_type`	Line type for the dotted lines (default: "dotted").
`vline_color`	Color for vertical lines separating clusters (default: "grey80").
`vline_type`	Line type for vertical lines separating clusters (default: "dashed").
`label_font_size`	Font size for the Level2 labels (default: 3).
`label_font_face`	Font face for the Level2 labels (default: "bold").
`pathway_font_size`	Font size for pathway labels (default: 2.5).
`pathway_font_face`	Font face for pathway labels (default: "italic").
`legend_position`	Position of the legend (default: "right").
`x_pathway_offset`	Offset to control the x-axis positioning of pathways (default: 0.3).
`label_x_size`	Font size for the x labels (default: 6).
`plot_margins`	Numeric vector of length 4 to control plot margins (default: c(5, 200, 10, 250)).