FeaturePlot_DualAssay: Customize FeaturePlot of two assays

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Customize FeaturePlot of two assays

Description

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

Usage

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

## Not run: 
FeaturePlot_DualAssay(seurat_object = object, features = "Cx3cr1", assay1 = "RAW", assay2 = "RNA",
colors_use = viridis_plasma_dark_high, na_color = "lightgray")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.