plotmclust: plotmclust

View source: R/plotmclust.R

plotmclustR Documentation

plotmclust

Description

Plot the model-based clustering results

Usage

plotmclust(
  mclustobj,
  x = 1,
  y = 2,
  MSTorder = NULL,
  show_tree = T,
  show_full_tree = T,
  show_cell_names = F,
  cell_name_size = 3,
  cell_point_size = 3,
  markerexpr = NULL,
  showcluster = T
)

Arguments

mclustobj

The exact output of exprmclust function.

x

The column of data after dimension reduction to be plotted on the horizontal axis.

y

The column of data after dimension reduction to be plotted on the vertical axis.

MSTorder

The arbitrary order of cluster to be shown on the plot.

show_tree

Whether to show the links between cells connected in the minimum spanning tree.

show_full_tree

Whether to show the full tree or not. Only useful when show_tree=T. Overrides MSTorder.

show_cell_names

Whether to draw the name of each cell in the plot.

cell_name_size

The size of cell name labels if show_cell_names is TRUE.

cell_point_size

The size of cell point.

markerexpr

The gene expression used to define the size of nodes.

Details

This function will plot the gene expression data after dimension reduction and show the clustering results.

Value

A ggplot2 object.

Author(s)

Zhicheng Ji, Hongkai Ji <zji4@zji4.edu>

Examples

data(lpsdata)
procdata <- preprocess(lpsdata)
lpsmclust <- exprmclust(procdata)
plotmclust(lpsmclust)

zji90/TSCAN documentation built on Sept. 14, 2022, 10:56 a.m.