Highlights the cells belonging to any number of top clonotypes or of specifically selected clonotypes from one or more samples or groups in a GEX dimensional reduction.
VDJ_GEX_overlay_clones(
GEX,
reduction,
n.clones,
clones.to.plot,
by.sample,
by.other.group,
ncol.facet,
pt.size,
clone.colors,
others.color,
split.plot.and.legend,
platypus.version
)A single seurat object from VDJ_GEX_matrix, which also includes VDJ information in the metadata (set integrate.VDJ.to.GEX to TRUE in the VDJ_GEX_matrix function) (VDJ_GEX_matrix.output[[2]]) ! Clone ids and frequencies are drawn from the columns "clonotype_id" and "clonotype_frequency"
Character. Defaults to "umap". Name of the reduction to overlay clones on. Can be "pca", "umap", "tsne"
Integer. Defaults to 5. To PLOT TOP N CLONES. Number of Top clones to plot. If either by.sample or by.group is TRUE, n.clones clones from each sample or group will be overlayed
Character. Alternative to n.clones. TO PLOT SPECIFIC CLONES. Must reference a column in the GEX@meta.data filled with TRUE and FALSE. Entries with TRUE label are plotted. Such a column may be generated using GEX@metadata$clones_to_plot_column <- GEX@metadata$Some_cell_identifier == "Interesting"
Boolean. Defaults to FALSE. Whether to overlay clones by sample. If set to TRUE this will generate a facet_wrap plot with as many facets as samples.
Character string. Defaults to "none". Must be a valid column name of the metadata of the input seurat object. If so, this will generate a facet_wrap plot with as many facets unique entries in the specified column. This may be useful to plot cell type specific clones
Integer. Defaults to 2. Number of columns in the facet_wrap plot if by.sample or by.group is TRUE
Numeric. Defaults to 1. Size of points in DimPlot. Passed to Seurat::DimPlot
Character vector. Defaults to rainbow(n.clones). Colors to use for individual clones. One can provide either a vector of length n.clones or a of length Nr. of samples/groups \* n.clones. In case that a vector of length n.clones is provided and by.group or by.sample is TRUE, colors are repeated for each sample/group
Character. Color for cells that are not selected i.e. not part of the overlayed clonotypes. Defaults to "grey80". To hide the rest of the umap set to "white"
Boolean. Defaults to FALSE. Whether to return the plot and the legend separately as a list. This can be useful if legends get large and distort the actual plots. The packages gridExtra and cowplot are required for this. If set to TRUE a list is returned where out[[1]] is the plot which can be printed just by executing out[[1]]; out[[2]] is the legend, which can be printed either using plot(out[[2]]) or grid.arrange(out[[2]])
Character. At the moment this function runs only on the output of the VDJ_GEX_matrix function meaning that it is exclusively part of Platypus "v3". With further updates the functionality will be extended.
A ggplot object or a list of a ggplot and a gtable legend (if split.plot.and.legend \=\= TRUE). Theme, colors etc. may be changed directly by adding new elements to this output (e.g. out \+ theme_minimal())
#To return a single plot with top clones across samples
overlay_clones_plot <- VDJ_GEX_overlay_clones(
GEX = Platypus::small_vgm[[2]], reduction = "umap"
,n.clones = 5, by.sample = FALSE
,by.other.group = "none", pt.size = 1,split.plot.and.legend = FALSE)
#> Using clonotype_id_10x column
#> Scale for 'colour' is already present. Adding another scale for 'colour',
#> which will replace the existing scale.
#To return a facet plot with top clones for each sample
overlay_clones_plot <- VDJ_GEX_overlay_clones(
GEX = Platypus::small_vgm[[2]], reduction = "umap"
,n.clones = 5, by.sample = TRUE, by.other.group = "none"
,pt.size = 1,ncol.facet = 2, split.plot.and.legend = FALSE)
#> Using clonotype_id_10x column
#To return a facet plot and the legend separately with top clones for each group
overlay_clones_plot <- VDJ_GEX_overlay_clones(
GEX = Platypus::small_vgm[[2]], reduction = "umap"
,n.clones = 5, by.sample = TRUE, by.other.group = "group_id", pt.size = 1
,ncol.facet = 2, split.plot.and.legend = TRUE)
#> Using clonotype_id_10x column
#To print both:
#overlay_clones_plot[[1]] #Plot
#gridExtra::grid.arrange(overlay_clones_plot[[2]]) #Legend
#To save, ggsave() is applicable to both
#To return a single plot with selected clones
#add a clonotype_to_plot column
#GEX@meta.data$clonotype_to_plot <- GEX$VJ_vgene == "TRAV5-1"
#Column with TRUE for all clones with a particular V gene
#overlay_clones_plot <- VDJ_GEX_overlay_clones(GEX = GEX, reduction = "umap"
#, clones.to.plot = "clonotype_to_plot", by.sample = TRUE, by.other.group = "none"
#, split.plot.and.legend = FALSE, pt.size = 1.5)