Create Plot with meta data variable of interest highlighted
Cell_Highlight_Plot(
seurat_object,
cells_highlight,
highlight_color = NULL,
background_color = "lightgray",
pt.size = NULL,
aspect_ratio = NULL,
figure_plot = FALSE,
raster = NULL,
raster.dpi = c(512, 512),
label = FALSE,
split.by = NULL,
split_seurat = FALSE,
ggplot_default_colors = FALSE,
...
)Arguments
- seurat_object
Seurat object name.
- cells_highlight
Cell names to highlight in named list.
- highlight_color
Color to highlight cells.
- background_color
non-highlighted cell colors (default is "lightgray")..
- pt.size
point size for both highlighted cluster and background.
- aspect_ratio
Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.
- figure_plot
logical. Whether to remove the axes and plot with legend on left of plot denoting axes labels. (Default is FALSE). Requires
split_seurat = TRUE.- raster
Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
- raster.dpi
Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
- label
Whether to label the highlighted meta data variable(s). Default is FALSE.
- split.by
Variable in
@meta.datato split the plot by.- split_seurat
logical. Whether or not to display split plots like Seurat (shared y axis) or as individual plots in layout. Default is FALSE.
- ggplot_default_colors
logical. If
highlight_color = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.- ...
Extra parameters passed to
DimPlot.
Value
A ggplot object
Examples
library(Seurat)
# Creating example non-overlapping vectors of cells
MS4A1 <- WhichCells(object = pbmc_small, expression = MS4A1 > 4)
GZMB <- WhichCells(object = pbmc_small, expression = GZMB > 4)
# Format as named list
cells <- list("MS4A1" = MS4A1,
"GZMB" = GZMB)
Cell_Highlight_Plot(seurat_object = pbmc_small, cells_highlight = cells)
