FactoWrapper: FactoMiner wrapper used by Shiny_DE_Viz for PCA/HCPC of...

View source: R/FactoWrapper.R

FactoWrapperR Documentation

FactoMiner wrapper used by Shiny_DE_Viz for PCA/HCPC of samples and genes

Description

FactoMiner wrapper used by Shiny_DE_Viz for PCA/HCPC of samples and genes

Usage

FactoWrapper(
  Output_DEseq2 = NULL,
  biplot = TRUE,
  readouts = 1,
  Top_var = 10,
  ellipse.level = 0.5,
  ellipse.alpha = 0.5,
  habillage_selection = "clust",
  label_sel = c("ind", "var"),
  pointsize = 1,
  labelsize = 1,
  selected_contrast = 1
)

Arguments

Output_DEseq2

R object generated by DEseq2_export function

biplot

Boolean value. If TRUE (Default), both individuals and variables will be shown on the plot. If FALSE, only individuals will be plotted.

readouts

either "rlog" (default) or "vsd" indicating the variance stabilization method preferred for visualization.

Top_var

a numeric value indicating the number of top contributing genes to show on the biplot.

ellipse.level

numeric value for ellipse size, from 0 to 1.0

ellipse.alpha

numeric value for ellipse transparency, from 0 to 1.0.

habillage_selection

string indicating the grouping to be shown. Default is "clust", which represents the HCPC ward clusters.

label_sel

String indicating if individuals "ind" and variables "var" should be labeled on the biplot.

pointsize

numeric value for point size.

labelsize

numeric value for label size.

selected_contrast

string indicating the DE contrast to be explored.

Value

FactoMiner plot showing HCPC of genes, samples, and conditions

Examples

Example_Hotgenes_dir<-system.file("extdata",
"Example_Hotgenes.Rdata",
package = "Hotgenes", mustWork = TRUE)
load(Example_Hotgenes_dir)
FactoWrapper(Example_Hotgenes)

Rvirgenslane/Hotgenes documentation built on June 15, 2024, 2:16 a.m.