MakeAnnotation: MakeAnnotation

In bicciatolab/PoPsicleR: Pipeline of Preprocessing for Single Cell Experiment

MakeAnnotation

Description

MakeAnnotation annotates cells using SingleR and scMCA built-in references.

For human samples, annotation is performed basing on the Human Primary Cell Atlas (HPCA) and the Blueprint Encode (BpEn) references from celldex and SingleR packages.

For mouse samples, annotation is performed according to mouse bulk RNA-seq datasets (Mouse RNA-seq) and Immunological Genome Project (ImmGen) references from SingleR, and the single-cell Mouse Cell Atlas (scMCA) reference.

Annotations are displayed on PCA, UMAP and TSNE embeddings, and evaluated through further graphs.

Usage

MakeAnnotation(UMI, organism=c("human","mouse"), marker.list='none', thresh=20, cluster_res=NULL, out_folder=getwd())

Arguments

UMI	The input umi object generated via CalculateCluster function
organism	The organism on which perfom the analysis. Can be human or mouse.
marker.list	Markers list used for the plots. Must be the same used in CalculateCluster. Default uses proprietary lists.
thresh	Rare population number threshold. Default is 20
cluster_res	Defines on which cluster resolution perform the annotation. Must be a clustering resolution already calculated by CalculateCluster in the previous step. Default is NULL.
out_folder	Output folder. Default is the working directory

Details

MakeAnnotation returns several graphs in the "04.Annotation" dedicated subfolder:

graphs 04a, show single-cell annotations for each reference on reduced spaces projections (t-SNE and UMAP). Cells are colored according to the assigned cell type.

graphs 04b, show cluster annotations for SingleR references on reduced spaces projections (t-SNE and UMAP). Cells are colored according to the clustering and labeled basing on the assigned cell type.

graphs 04c, report single-cell annotations for each reference on reduced spaces projections (t-SNE and UMAP). Cells are colored in red according to the assigned cell type. Each cell type is displayed individually.

graphs 04d, return dot plots reporting, in the cell types assigned using the different references, the markers genelist expression.

graphs 04e, are pie-chart plots displaying, for each cluster, the proportion of cells annotated with a specific label based on the different references.

Value

Returns a Seurat Object after annotation.

Author(s)

Jimmy Caroli, Francesco Grandi

Examples

MakeAnnotation(umi_object, organism="human", marker.list= "markers.txt", cluster_res=0.8)

bicciatolab/PoPsicleR documentation built on May 7, 2024, 7:26 a.m.