VDJ_GEX_overlay_clones: Overlay clones on GEX projection

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

Overlay clones on GEX projection

Description

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.

Usage

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
)

Arguments

GEX	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"
reduction	Character. Defaults to "umap". Name of the reduction to overlay clones on. Can be "pca", "umap", "tsne"
n.clones	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
clones.to.plot	Character. Alternative to n.clones. TO PLOT SPECIFIC CLONES. Must reference a column in the [e-mail] 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"
by.sample	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.
by.other.group	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
ncol.facet	Integer. Defaults to 2. Number of columns in the facet_wrap plot if by.sample or by.group is TRUE
pt.size	Numeric. Defaults to 1. Size of points in DimPlot. Passed to Seurat::DimPlot
clone.colors	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
others.color	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"
split.plot.and.legend	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]])
platypus.version	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.

Value

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())

Examples

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)

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)

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)

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.