Customize FeaturePlot of two assays — FeaturePlot

Create Custom FeaturePlots and preserve scale (no binning) from same features in two assays simultaneously. Intended for plotting same modality present in two assays.

FeaturePlot_DualAssay(
  seurat_object,
  features,
  assay1 = "RAW",
  assay2 = "RNA",
  colors_use = viridis_plasma_dark_high,
  colors_use_assay2 = NULL,
  na_color = "lightgray",
  order = TRUE,
  pt.size = NULL,
  aspect_ratio = NULL,
  reduction = NULL,
  na_cutoff = 1e-09,
  raster = NULL,
  raster.dpi = c(512, 512),
  layer = "data",
  num_columns = NULL,
  alpha_exp = NULL,
  alpha_na_exp = NULL,
  ...
)

Arguments

seurat_object: Seurat object name.
features: Feature(s) to plot.
assay1: name of assay one. Default is "RAW" as featured in Create_CellBender_Merged_Seurat
assay2: name of assay two Default is "RNA" as featured in Create_CellBender_Merged_Seurat
colors_use: list of colors or color palette to use.
colors_use_assay2: optional, a second color palette to use for the second assay.
na_color: color to use for points below lower limit.
order: whether to move positive cells to the top (default = TRUE).
pt.size: Adjust point size for plotting.
aspect_ratio: Control the aspect ratio (y:x axes ratio length). Must be numeric value; Default is NULL.
reduction: Dimensionality Reduction to use (if NULL then defaults to Object default).
na_cutoff: Value to use as minimum expression cutoff. To set no cutoff set to NA.
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).
layer: Which layer to pull expression data from? Default is "data".
num_columns: Number of columns in plot layout. If number of features > 1 then num_columns dictates the number of columns in overall layout (num_columns = 1 means stacked layout & num_columns = 2 means adjacent layout).
alpha_exp: new alpha level to apply to expressing cell color palette (colors_use). Must be value between 0-1.
alpha_na_exp: new alpha level to apply to non-expressing cell color palette (na_color). Must be value between 0-1.
...: Extra parameters passed to FeaturePlot.

Value

A ggplot object

Examples

if (FALSE) {
FeaturePlot_DualAssay(seurat_object = object, features = "Cx3cr1", assay1 = "RAW", assay2 = "RNA",
colors_use = viridis_plasma_dark_high, na_color = "lightgray")
}