FeaturePlot_DualAssay {scCustomize} | R Documentation |
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,
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 |
assay2 |
name of assay two Default is "RNA" as featured in |
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 |
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 |
|
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 |
alpha_exp |
new alpha level to apply to expressing cell color palette ( |
alpha_na_exp |
new alpha level to apply to non-expressing cell color palette ( |
... |
Extra parameters passed to |
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)