Customize FeaturePlot of two assays

Source: R/Seurat_Plotting.R

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,
  na_color = "lightgray",
  order = TRUE,
  pt.size = NULL,
  aspect_ratio = NULL,
  reduction = NULL,
  na_cutoff = 1e-09,
  raster = NULL,
  raster.dpi = c(512, 512),
  slot = deprecated(),
  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.

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).

slot

[Deprecated] soft-deprecated. See layer

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")
}