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.
VDJ_GEX_expansion(
GEX.list,
VDJ.GEX.integrate.list,
highlight.isotype,
highlight.number
)The output of the automate_GEX function.
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.
(Optional) isotype to plot, choose between ["None","A","E","M","G","G1","G2A","G2B","G2C","G3"]. Default is None.
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.
ggplot2 plot that breaks down clonotype membership per cluster for the specified input clones.
if (FALSE) {
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)
}