Description Usage Arguments Details Value Functions Examples
make_hexbin
returns a
SingleCellExperiment
or
Seuratclass
object of binned hexagon cells.
1 2 3 4 5 6 7  make_hexbin(sce, nbins = 80, dimension_reduction = "UMAP", use_dims = c(1, 2))
## S4 method for signature 'SingleCellExperiment'
make_hexbin(sce, nbins = 80, dimension_reduction = "UMAP", use_dims = c(1, 2))
## S4 method for signature 'Seurat'
make_hexbin(sce, nbins = 80, dimension_reduction = "UMAP", use_dims = c(1, 2))

sce 
A 
nbins 
The number of bins partitioning the range of the first component of the chosen dimension reduction. 
dimension_reduction 
A string indicating the reduced dimension result to calculate hexagon cell representation of. 
use_dims 
A vector of two integers specifying the dimensions used. 
This function bins observations with computed reduced dimension
results into hexagon cells. For a Seuratclass
object the
results from this function are stored in @misc
. For a
SingleCellExperiment
as a list in the @metadata
. The list contains two items. The first
item stores a vector specifying the hexagon ID for each
observation. The second item stores a matrix with the x and y positions of
the hexagon cells and the number of observations in each of them.
A SingleCellExperiment
or
Seuratclass
object.
make_hexbin,SingleCellExperimentmethod
: Bivariate binning of SingleCellExperiment
into hexagon cells.
make_hexbin,Seuratmethod
: Bivariate binning of Seurat
into hexagon cells.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  # For Seurat object
library(Seurat)
data("pbmc_small")
pbmc_small < make_hexbin(pbmc_small, 10, dimension_reduction = "PCA")
# For SingleCellExperiment object
## Not run:
library(TENxPBMCData)
library(scater)
tenx_pbmc3k < TENxPBMCData(dataset = "pbmc3k")
rm_ind < calculateAverage(tenx_pbmc3k) < 0.1
tenx_pbmc3k < tenx_pbmc3k[!rm_ind, ]
tenx_pbmc3k < logNormCounts(tenx_pbmc3k)
tenx_pbmc3k < runPCA(tenx_pbmc3k)
tenx_pbmc3k < make_hexbin(tenx_pbmc3k, 80, dimension_reduction = "PCA")
## End(Not run)

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