DeduceRelationship: ELeFHAnt Deduce Relationship

In praneet1988/ELeFHAnt: Ensemble Learning for Harmonization and Annotation of Single Cells

ELeFHAnt Deduce Relationship

Description

Deduce Relationship is a function that hels deduce relationships among celltypes/annotationCol between two datasets. It requires two datasets (both processed Seurat Objects). Obtain relationships among metadata of interest. Function outputs a heatmap with annotation from dataset1 y-axis and annotation from dataset2 on x-axis.

Usage

DeduceRelationship(
  reference1 = NULL,
  reference2 = NULL,
  downsample = TRUE,
  downsample_to = 1000,
  selectvarfeatures = 2000,
  ntree = 500,
  annotationCol_ref1 = "Celltypes",
  annotationCol_ref2 = "Celltypes"
)

Arguments

reference1	a processed Seurat Object with Celltypes column in metadata
reference2	a processed seurat object with Celltypes column in metadata
downsample	logical Indicator (TRUE or FALSE) to downsample reference1 and reference2, enabling fast computation
downsample_to	a numerical value > 1 to downsample cells Default: 1000
selectvarfeatures	number of variable features to select while training (Default: 2000)
ntree	number of trees randomForest classifier should build (Default: 500)
annotationCol_ref1	Name of column in metdata which has Celltypes information Default: Celltypes in reference1
annotationCol_ref2	Name of column in metdata which has Celltypes information Default: Celltypes in reference2

Value

ggplot2 heatmap object and heatmap is automatically saved

Author(s)

Praneet Chaturvedi & Konrad Thorner

praneet1988/ELeFHAnt documentation built on July 20, 2022, 7:29 p.m.