do_ChordDiagramPlot: Generate a Chord diagram.

In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Generate a Chord diagram.

Description

Generate a Chord diagram.

Usage

do_ChordDiagramPlot(
  sample = NULL,
  from = NULL,
  to = NULL,
  colors.from = NULL,
  colors.to = NULL,
  big.gap = 10,
  small.gap = 1,
  link.border.color = NA,
  link.border.width = 1,
  highlight_group = NULL,
  alpha.highlight = 25,
  link.sort = NULL,
  link.decreasing = TRUE,
  z_index = FALSE,
  self.link = 1,
  symmetric = FALSE,
  directional = 1,
  direction.type = c("diffHeight", "arrows"),
  link.arr.type = "big.arrow",
  scale = FALSE,
  alignment = "default",
  annotationTrack = c("grid", "axis"),
  padding_labels = 4,
  ...
)

Arguments

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
from, to	character | Categorical metadata variable to be used as origin and end points of the interactions.
colors.from, colors.to	named_vector | Named vector of colors corresponding to the unique values of "from" and "to".
big.gap	numeric | Space between the groups in "from" and "to".
small.gap	numeric | Space within the groups.
link.border.color	character | Color for the border of the links. NA = no color.
link.border.width	numeric | Width of the border line of the links.
highlight_group	character | A value from from that will be used to highlight only the links coming from it.
alpha.highlight	numeric | A value between 00 (double digits) and 99 to depict the alpha of the highlighted links. No transparency needs "FF"
link.sort	pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
link.decreasing	pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
z_index	logical | Whether to bring the bigger links to the top.
self.link	numeric | Behavior of the links. One of: 1: Prevents self linking. 2: Allows self linking.
symmetric	pass to chordDiagramFromMatrix
directional	numeric | Set the direction of the links. One of: 0: Non-directional data. 1: Links go from "from" to "to". -1: Links go from "to" to "from". 2: Links go in both directions.
direction.type	character | How to display the directions. One of: diffHeight: Sets a line at the origin of the group showing to how many groups and in which proportion this group is linked to. arrows: Sets the connection as arrows. both: Sets up both behaviors. Use as: c("diffHeight", "arrows").
link.arr.type	character | Sets the appearance of the arrows. One of: triangle: Arrow with a triangle tip at the end displayed on top of the link. big.arrow: The link itself ends in a triangle shape.
scale	logical | Whether to put all nodes the same width.
alignment	character | How to align the diagram. One of: default: Allows circlize to set up the plot as it sees fit. horizontal: Sets the break between "from" and "to" groups on the horizontal axis. vertical: Sets the break between "from" and "to" groups on the vertical axis.
annotationTrack	pass to chordDiagramFromMatrix or chordDiagramFromDataFrame
padding_labels	numeric | Number of extra padding (white spaces) of the labels so that they do not overlap with the scales.
...	For internal use only.

Value

A circlize plot.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_ChordDiagramPlot", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds", package = "SCpubr"))

    # Basic chord diagram.
    sample$assignment <- ifelse(sample$seurat_clusters %in% c("0", "4", "7"), "A", "B")
    sample$assignment[sample$seurat_clusters %in% c("1", "2")] <- "C"
    sample$assignment[sample$seurat_clusters %in% c("10", "5")] <- "D"
    sample$assignment[sample$seurat_clusters %in% c("8", "9")] <- "E"

    p <- SCpubr::do_ChordDiagramPlot(sample = sample,
                                     from = "seurat_clusters",
                                     to = "assignment")

    p

  } else if (base::isFALSE(value)){
    message("This function can not be used without its suggested packages.")
    message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
  }

enblacar/SCpubr documentation built on Aug. 25, 2024, 9:45 p.m.