plot_MDS: Plots MDS results Plots MDS results of trees for each...
In svteichman/TreeVizPackage: Tree Visualization Package

plot_MDS

R Documentation

Plots MDS results Plots MDS results of trees for each distance.

Description

Plots MDS results Plots MDS results of trees for each distance.

Usage

plot_MDS(
  df,
  consensus = NULL,
  group = NULL,
  title = "MDS of Gene Tree Distances",
  x_dim = "scale_x_dim",
  y_dim = "scale_y_dim",
  show_legend = FALSE,
  legend_lab = NULL,
  scales_arg = "free",
  single_method = FALSE,
  gene_names = NULL
)

Arguments

`df`	A dataframe with the first two MDS coordinates for a set of trees and distances.
`consensus`	An optional argument specifying whether the first tree is a consensus tree, and if so the name of the consensus tree.
`group`	An optional variable to color points by.
`title`	An optional paramater to change the plot title.
`x_dim`	The name of the variable within the dataframe that specifies the value on the x axis.
`y_dim`	The name of the variable within the dataframe that specifies the value on the y axis.
`show_legend`	A boolean about whether or not to show a legend.
`legend_lab`	A label for the legend (NULL if not specified).
`scales_arg`	An optional argument about whether the scales should be fixed or free. Set to free by default.
`single_method`	True if the dataframe only includes data from a single distance metric.
`gene_names`	An optional variable to label genes by.