View source: R/GEX_visualize_clones.R
GEX_visualize_clones | R Documentation |
!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 )
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". |
concatenated ggplot2 plot with selected clonotypes highlighted (if None, the coloring is according to the clustering).
## Not run: GEX_visualize_clones(GEX.list=automate_GEX.output, VDJ.per.clone=VDJ_per_clone.output, highlight.type="clonotype", highlight.number=1:4, reduction="umap") ## End(Not run)
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