plot_pca: Multiple options for plotting descriptive statistics from...

In hsaxe/Omics-Analyst: Functions to facilitate the statistical analysis of omics data.

Multiple options for plotting descriptive statistics from PCA. Takes a numeric data frame as input.

Description

Multiple options for plotting descriptive statistics from PCA. Takes a numeric data frame as input.

Usage

plot_pca(
  dat,
  metadata = NULL,
  join_by_name = "Sample",
  plotting_factors_name = Group,
  plotting_factors_in = "col_names",
  x = "PC1",
  y = "PC2",
  scale = T,
  center = T,
  color = "Group",
  fill = "Group",
  plot_type = "2D",
  points_label = "Group",
  summarise_for_scatter = T,
  sep = "-"
)

Arguments

dat	A data.frame
metadata	Optional data frame with metadata for filling, coloring, or plotting PCA results against.
join_by_name	Name of column in metadata that matches rownames/colnames of data. Used to join metadata with data. This is usually sample names. For example, sample1.1, sample1.2, etc.
plotting_factors_name	Name for factor you want to plot. Is made by removing two characters from the end of 'join_by_name' variable. For example, sample1.1, sample1.2 and sample2.1, sample2.2 in this variable become sample1, sample1 and sample2, sample2. Used for coloring, filling, and grouping of plot. Default name is Group
plotting_factors_in	Location of plotting factors. Options are either 'col_names' or 'row_names'.
x	What do you want to plot on the x-axis? Default is 'PC1'
y	What do you want to plot on the y-axis? Default is 'PC2'
scale	Logical. Scale data? Default is TRUE
center	Logical. Center data? Default is TRUE
color	Which variable to color by? Default is 'Group'.
fill	Which variable to fill by? Default is 'Group'.
plot_type	One of three options: '2D', 'boxplot', or 'scatter'. Default is '2D'.
points_label	Which variable to label points by? Default is 'Group".
summarise_for_scatter	Logical. Plotting factors can sometimes contain psuedoreplication which inflates the p-value of this scatterplot. This option will summarize the plotting factors by mean, removing psuedoreplication for a more realistic p-value. Default is TRUE.
sep	Desired separator for sample names in data to match that of metadata

hsaxe/Omics-Analyst documentation built on Sept. 7, 2024, 12:15 p.m.