This function plots cell density in histological space as 2D histograms, especially helpful for larger smFISH-based datasets.

## Usage

```
plotCellBin2D(
sfe,
sample_id = "all",
bins = 200,
binwidth = NULL,
hex = FALSE,
ncol = NULL,
bbox = NULL
)
```

## Arguments

- sfe
A

`SpatialFeatureExperiment`

object.- sample_id
Sample(s) in the SFE object whose cells/spots to use. Can be "all" to compute metric for all samples; the metric is computed separately for each sample.

- bins
Number of bins. Can be a vector of length 2 to specify for x and y axes separately.

- binwidth
Width of bins, passed to

`geom_bin2d`

or`geom_hex`

.- hex
Logical, whether to use hexagonal bins.

- ncol
Number of columns if plotting multiple features. Defaults to

`NULL`

, which means using the same logic as`facet_wrap`

, which is used by`patchwork`

's`wrap_plots`

by default.- bbox
A bounding box to specify a smaller region to plot, useful when the dataset is large. Can be a named numeric vector with names "xmin", "xmax", "ymin", and "ymax", in any order. If plotting multiple samples, it should be a matrix with sample IDs as column names and "xmin", "ymin", "xmax", and "ymax" as row names. If multiple samples are plotted but

`bbox`

is a vector rather than a matrix, then the same bounding box will be used for all samples. You may see points at the edge of the geometries if the intersection between the bounding box and a geometry happens to be a point there. If`NULL`

, then the entire tissue is plotted.

## Examples

```
library(SFEData)
sfe <- HeNSCLCData()
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
plotCellBin2D(sfe)
```