Platypus V2 GEX and VDJ integration for visualizing clone clustering

!Only for platypus version v2. For platypus v3 refer to: VDJ_GEX_overlay_clones() Visualize selected clonotypes on the tSNE or UMAP projection.

GEX_visualize_clones(
  GEX.list,
  VDJ.GEX.integrate.list,
  highlight.type,
  highlight.number,
  reduction
)

Arguments

GEX.list

list of Seurat objects, output of the automate_GEX function.

VDJ.GEX.integrate.list

Output of the VDJ_GEX_integrate function.

highlight.type

(Optional) either "None" if representation highlighted by cluster, "clonotype" if want to highlight most expanded clonotypes, or "sample" if several samples are within the same Seurat object. Default is None.

highlight.number

(Optional) an integer or list of integers representing the number of most expanded clonotypes or samples one wants to select eg 4 to highlight the 4th most expanded clonotype or 2:5 to highlight the top 2 to top 5 most expanded clonotype. Only compatible with highlight.type "clonotype" or "sample", will be ignored if type is "None". Default is 1.

reduction

(Optional) Reduction to plot, either "tsne", "umap", or "harmony". Default is "tsne".

Value

concatenated ggplot2 plot with selected clonotypes highlighted (if None, the coloring is according to the clustering).

Examples

if (FALSE) {
GEX_visualize_clones(GEX.list=automate_GEX.output,
 VDJ.per.clone=VDJ_per_clone.output,
 highlight.type="clonotype",
 highlight.number=1:4,
 reduction="umap")
}