make.network.plot: Draw network diagram

In sydneycytometry/Spectre: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data.

Description

Method to draw a network diagram. This rely on a clustering performed by ChronoClust.

Usage

make.network.plot(dat, timepoint.col, timepoints, cluster.col, marker.cols,
node.size = 13, arrow.length = 3, arrow.head.gap = 4, standard.colours = 'Spectral')

Arguments

dat	NO DEFAULT. Data table. Dataset.
timepoint.col	NO DEFAULT. Column name which represents the time point of each cell (data point) in dat.
timepoints	NO DEFAULT. The time points (in order).
cluster.col	NO DEFAULT. Column denoting the cluster id.
marker.cols	NO DEFAULT. Vector of column names denoting the markers to plot.
node.size	DEFAULT = 'auto'. By default, set the size of the node to proportion of cells in the cluster. Set this to specific number if you want the node size to be the same regardless.
min.node.size	DEFAULT = 6. Minimum node size if node size is scaled to proportion of cells in cluster. Otherwise not used.
max.node.size	DEFAULT = 12. Maximum node size if node size is scaled to proportion of cells in cluster. Otherwise not used.
arrow.length	DEFAULT = 3. Length of the arrow connecting nodes.
arrow.head.gap	DEFAULT = 4. The gap between head of the arrow and node.
standard.colours	DEFAULT = "Spectral". Colour scheme for the markers. Spectral or Inferno or Viridis.

Author(s)

Givanna Putri, [e-mail]

sydneycytometry/Spectre documentation built on March 20, 2021, 2:15 a.m.