shinyPCAtools: Create an interactive Shiny app for PCAtools analysis and...

In j-andrews7/iBET: Interactive Bioinformatics Exploratory Tools

Create an interactive Shiny app for PCAtools analysis and results exploration

Description

Create an interactive Shiny app for PCAtools analysis and results exploration

Usage

shinyPCAtools(
  mat,
  metadata,
  removeVar = 0.3,
  scale = FALSE,
  center = TRUE,
  color.by = NULL,
  shape.by = NULL,
  annot.by = NULL,
  height = 850
)

Arguments

mat	A matrix with features as rows and samples as columns.
metadata	A dataframe containing sample metadata. The rownames must match the column names of the matrix.
removeVar	Remove this % of variables based on low variance.
scale	Scale the data? Same as prcomp() 'scale' parameter.
center	Center the data before performing PCA? Same as prcomp() 'center' parameter.
color.by	A string containing the name of a sample metadata variable to be used to color points.
shape.by	A string containing the name of a sample metadata variable to be used to shape points.
annot.by	A string or character vector containing the names of sample metadata variables to be used for hover text.
height	Number indicating height of app in pixels.

Details

Features with no variation will be removed prior to pca being run.

Value

A Shiny app wrapped around most PCAtools functions and plots.

Author(s)

Jared Andrews

See Also

pca, screeplot, biplot, pairsplot, eigencorplot.

j-andrews7/iBET documentation built on April 17, 2025, 2:55 p.m.