gg_PCoA: PCoA plot via cmdscale

In mrmtshmp/ExploratoryDataAnalysis: Make plots for explanatory data analyses

Description

PCoA plot via cmdscale

Usage

gg_PCoA(
  distmat,
  groups,
  ggplot_theme = summ_plot_theme,
  axes = c("CS1", "CS2"),
  k_pc = c(1, 2),
  overlay = FALSE,
  labels = "sample_ID",
  title = "PCoA plot using by MDS",
  legend.name = "Cluster",
  jitter.v = 0.3,
  jitter.h = 0.3,
  size = 2,
  alpha = 0.7
)

Arguments

distmat	<object; input data; mandatory> An object with dist-class.
groups	<character; output> A varible used forcolor coding.
ggplot_theme	<object; proccessing>
axes	<character strings; output; prefix = c("CS11","CS2")> Labels for x and y axes.
k_pc	<numeric>
overlay	<logical; output; prefix =FALSE> Print subject IDs on respective plots?
labels	<; processing; prefix =2> Colour brewer setting
title	<object; input data; mandatory> A data.frame with features as column and subjects as rows.
legend.name	<object; input data> A data.frame with 2 column of a feature and subject ID. This ID must be identical with of count_table.
jitter.v	<numeric; proccessing; prefix=0.3>
jitter.h	<numeric; proccessing; prefix=0.3>
size	<numeric; proccessing; prefix=2>
alpha	<numeric; proccessing; prefix=0.7>

mrmtshmp/ExploratoryDataAnalysis documentation built on Oct. 6, 2020, 8 a.m.