VDJ_GEX_expansion: Platypus V2 utility

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Platypus V2 utility

Description

only Platypus v2 Integrates VDJ and gene expression libraries by providing cluster membership seq_per_vdj object. Output will plot which transcriptional cluster (GEX) that the cells of a given clonotype are found in.

Usage

VDJ_GEX_expansion(
  GEX.list,
  VDJ.GEX.integrate.list,
  highlight.isotype,
  highlight.number
)

Arguments

GEX.list	The output of the automate_GEX function.
VDJ.GEX.integrate.list	Output from VDJ_GEX_integrate function. This object needs to have the GEX and VDJ information combined and integrated. This should be on the CLONAL level from the VDJ_GEX_integrate function.
highlight.isotype	(Optional) isotype to plot, choose between ["None","A","E","M","G","G1","G2A","G2B","G2C","G3"]. Default is None.
highlight.number	A vector corresponding to the rank of the clones that should be specified. Default is set to "20", which will present the cluster distribution for the top 20 clones.

Value

ggplot2 plot that breaks down clonotype membership per cluster for the specified input clones.

Examples

## Not run: 
vdj.gex.expansion <- VDJ_GEX_expansion(GEX.list=GEX.list.output[[1]]
,VDJ.GEX.integrate.list=vdj.gex.integrate.output
,highlight.isotype = "None",highlight.number=1:20)

## End(Not run)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.