GraphPlot: GraphPlot

In zh542370159/SCP: Single Cell Pipeline

GraphPlot

Description

A function to plot a graph with nodes and edges.

Usage

GraphPlot(
  node,
  edge,
  transition = NULL,
  node_coord = c("x", "y"),
  node_group = NULL,
  node_palette = "Paired",
  node_palcolor = NULL,
  node_size = 4,
  node_alpha = 1,
  node_highlight = NULL,
  node_highlight_color = "red",
  label = FALSE,
  label.size = 3.5,
  label.fg = "white",
  label.bg = "black",
  label.bg.r = 0.1,
  label_insitu = FALSE,
  label_repel = FALSE,
  label_repulsion = 20,
  label_point_size = 1,
  label_point_color = "black",
  label_segment_color = "black",
  edge_threshold = 0.01,
  use_triangular = c("upper", "lower", "both"),
  edge_line = c("straight", "curved"),
  edge_line_curvature = 0.3,
  edge_line_angle = 90,
  edge_color = "grey40",
  edge_size = c(0.2, 1),
  edge_alpha = 0.5,
  edge_shorten = 0,
  edge_offset = 0,
  edge_highlight = NULL,
  edge_highlight_color = "red",
  transition_threshold = 0.01,
  transition_line = c("straight", "curved"),
  transition_line_curvature = 0.3,
  transition_line_angle = 90,
  transition_color = "black",
  transition_size = c(0.2, 1),
  transition_alpha = 1,
  transition_arrow_type = "closed",
  transition_arrow_angle = 20,
  transition_arrow_length = unit(0.02, "npc"),
  transition_shorten = 0.05,
  transition_offset = 0,
  transition_highlight = NULL,
  transition_highlight_color = "red",
  aspect.ratio = 1,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scp",
  theme_args = list(),
  return_layer = FALSE
)

Arguments

node	A data frame representing the nodes of the graph.
edge	A matrix representing the edges of the graph.
transition	A matrix representing the transitions between nodes.
node_coord	A character vector specifying the names of the columns in node that represent the x and y coordinates.
node_group	A character vector specifying the name of the column in node that represents the grouping of the nodes.
node_palette	A character vector specifying the name of the color palette for node groups.
node_palcolor	A character vector specifying the names of the colors for each node group.
node_size	A numeric value or column name of node specifying the size of the nodes.
node_alpha	A numeric value or column name of node specifying the transparency of the nodes.
node_highlight	A character vector specifying the names of nodes to highlight.
node_highlight_color	A character vector specifying the color for highlighting nodes.
label	A logical value indicating whether to show labels for the nodes.
label.size	A numeric value specifying the size of the labels.
label.fg	A character vector specifying the foreground color of the labels.
label.bg	A character vector specifying the background color of the labels.
label.bg.r	A numeric value specifying the background color transparency of the labels.
label_insitu	A logical value indicating whether to display the node group labels in situ or as numeric values.
label_repel	A logical value indicating whether to use force-directed label repulsion.
label_repulsion	A numeric value specifying the repulsion force for labels.
label_point_size	A numeric value specifying the size of the label points.
label_point_color	A character vector specifying the color of the label points.
label_segment_color	A character vector specifying the color for the label segments.
edge_threshold	A numeric value specifying the threshold for removing edges.
use_triangular	A character vector specifying which part of the edge matrix to use (upper, lower, both).
edge_line	A character vector specifying the type of line for edges (straight, curved).
edge_line_curvature	A numeric value specifying the curvature of curved edges.
edge_line_angle	A numeric value specifying the angle of curved edges.
edge_color	A character vector specifying the color of the edges.
edge_size	A numeric vector specifying the range of edge sizes.
edge_alpha	A numeric value specifying the transparency of the edges.
edge_shorten	A numeric value specifying the length of the edge shorten.
edge_offset	A numeric value specifying the length of the edge offset.
edge_highlight	A character vector specifying the names of edges to highlight.
edge_highlight_color	A character vector specifying the color for highlighting edges.
transition_threshold	A numeric value specifying the threshold for removing transitions.
transition_line	A character vector specifying the type of line for transitions (straight, curved).
transition_line_curvature	A numeric value specifying the curvature of curved transitions.
transition_line_angle	A numeric value specifying the angle of curved transitions.
transition_color	A character vector specifying the color of the transitions.
transition_size	A numeric vector specifying the range of transition sizes.
transition_alpha	A numeric value specifying the transparency of the transitions.
transition_arrow_type	A character vector specifying the type of arrow for transitions (closed, open).
transition_arrow_angle	A numeric value specifying the angle of the transition arrow.
transition_arrow_length	A numeric value specifying the length of the transition arrow.
transition_shorten	A numeric value specifying the length of the transition shorten.
transition_offset	A numeric value specifying the length of the transition offset.
transition_highlight	A character vector specifying the names of transitions to highlight.
transition_highlight_color	A character vector specifying the color for highlighting transitions.
aspect.ratio	A numeric value specifying the aspect ratio of the plot.
title	A character value specifying the title of the plot.
subtitle	A character value specifying the subtitle of the plot.
xlab	A character value specifying the label for the x-axis.
ylab	A character value specifying the label for the y-axis.
legend.position	A character value specifying the position of the legend.
legend.direction	A character value specifying the direction of the legend.
theme_use	A character value specifying the theme to use.
theme_args	A list of arguments to be passed to the theme.
return_layer	A logical value indicating whether to return the layers of the plot instead of the plot itself.

See Also

CellDimPlot

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.