Test_PCA_dim_Harmony: A Test_PCA_dim_Harmony Function

In parveendabas/SCA: What the Package Does (One Line, Title Case)

A Test_PCA_dim_Harmony Function

Description

This function allows you to compare different no. of PCAs for Harmony. Cluster Resolution is set to 0.1.

Usage

Test_PCA_dim_Harmony(
  Temp.object,
  saveDIR,
  IdentToBatchCorrect = "orig.ident",
  ThetaToBatchCorrect = 2,
  SuffixName = "Testing_PCA_Dim",
  ColNamesToPlot = ColNamesToPlot,
  ColPaletteToPlot = ColPaletteToPlot,
  mingenes = 500,
  PCAdimList = c(20, 25, 30, 40, 50),
  ClusOrder = ClusOrderFrom1,
  DownSamplePCA = 1000
)

Arguments

Temp.object	Seurat objects to be used for the QC plots.
saveDIR	Directory to save the plots.
IdentToBatchCorrect	Identity to be used for Harmony batch correction (Max 1)
ThetaToBatchCorrect	Theta values to be used while running harmony. Diversity clustering penalty parameter. Specify for each variable in group.by.vars. Default theta=2. theta=0 does not encourage any diversity. Larger values of theta result in more diverse clusters.
SuffixName	Suffix. to be added in the directory name as
ColNamesToPlot	Vector of identities to plot (Max = 3)
ColPaletteToPlot	list of color palettes to plot for the identities (Max = 3)
mingenes	minimum gene number that will be mentioned in the output file name
PCAdimList	Vector of the PCAs to be used for testing
DownSamplePCA	#Cells to plot in UMAP for PCA testing

Examples

Test_PCA_dim_Harmony()

parveendabas/SCA documentation built on Sept. 19, 2022, 8:31 a.m.