HighlightCellsOnSeuratPlot: HighlightCellsOnSeuratPlot

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

HighlightCellsOnSeuratPlot

Description

Can be used to highlight a set of cells from a seurat plot, such as overlaying specific clonotypes. Note: this uses ggnewscale::new_scale_color to enable multiple color scales. The original aesthetics are suffixed with '_new' (i.e. color_new). This has also only been tested thoroughly with DimPlots.

Usage

HighlightCellsOnSeuratPlot(
  seuratObj,
  seuratPlot,
  cellSelectField = "CloneNames",
  colorLegendLabel = "Clone",
  colorField = NA,
  dotColor = NA,
  pt.size = 1,
  shapeField = NA,
  dotShapes = NA,
  horizontalLegend = TRUE,
  resetLegendSize = TRUE,
  maxAllowableShapeValues = 6
)

Arguments

seuratObj	The seurat object
seuratPlot	The plot object, such as the result from DimPlot()
cellSelectField	The name of the field to select which cells to plot
colorLegendLabel	This is passed to labs(color = XXX) to label the legend
colorField	The name of the field to assign colors to the cells. This provides the option to use a different value from cellSelectField. If colorField and dotColor are NA, cellSelectField will be used.
dotColor	An optional string passed to geom_point(color = XX). This will assign all cells the same color. Ignored if colorField is provided.
pt.size	The size, passed to geom_point().
shapeField	If true, provided, these values will be used for shape. Note: if there are more than 6 unique values this will be ignored.
dotShapes	An optional vector of shape values passed to scale_shape_manual(values = XX). If dotShapes is provided, but shapeField is not, all cells will receive the same shape.
horizontalLegend	If true, theme(legend.box = "horizontal") is added to the plot. This can be useful if the original plot also has a legend (such as cluster names)
resetLegendSize	Using ggnewscale::new_scale_color seems to reset the dot size of the legend. If resetLegendSize=TRUE, the function will call "guides(colour_new = guide_legend(override.aes = list(size=3)))" to restore dot size to 3.
maxAllowableShapeValues	If shapes are used and there are more than this many values, all cells will receive the same shape.

bimberlabinternal/CellMembrane documentation built on Dec. 20, 2024, 11:13 p.m.