Plot colData and rowData with 2D histograms

To avoid overplotting in large datasets. The 2D histogram is more informative of point density on the plot than the scatter plot where there are so many points plotted that they effectively form a solid block.

Usage

plotColDataBin2D(
  sce,
  x,
  y,
  facet_by = NULL,
  subset = NULL,
  bins = 100,
  binwidth = NULL,
  hex = FALSE,
  name_true = NULL,
  name_false = NULL,
  ncol = NULL,
  ...
)

plotRowDataBin2D(
  sce,
  x,
  y,
  facet_by = NULL,
  subset = NULL,
  bins = 100,
  binwidth = NULL,
  hex = FALSE,
  name_true = NULL,
  name_false = NULL,
  ncol = NULL,
  ...
)

Arguments

sce

A SingleCellExperiment object.

x

Name of the column in colData or rowData to plot on the x axis of the plot.

y

Name of the column in colData or rowData to plot on the y axis of the plot.

facet_by

Column in colData or rowData to facet with.

subset

Name of a logical column in colData or rowData, indicating cells or genes to plot with a different palette. Since the 2D histogram is effectively an opaque heatmap, don't use this argument unless the two groups are largely non-overlapping in the variables being plotted.

bins

Numeric vector giving number of bins in both vertical and horizontal directions. Set to 100 by default.

binwidth

Numeric vector giving bin width in both vertical and horizontal directions. Overrides bins if both set.

hex

Logical, whether to use hexagon rather than rectangular bins. Requires the hexbin package.

name_true

Character, name to show on the legend for cells or genes indicated TRUE in the subset argument.

name_false

Character, name to show on the legend for cells or genes indicated FALSE in the subset argument.

ncol

If facetting, the number of columns of facets, passed to facet_wrap.

...

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Value

A ggplot object

Examples

library(SFEData)
sfe <- McKellarMuscleData()
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
sfe <- sfe[, sfe$in_tissue]
plotColDataBin2D(sfe, "nCounts", "nGenes")
#> Warning: plotCol/RowDataBin2D() was deprecated in Voyager 1.2.0.
#> ℹ Please use scater::plotCol/RowData() instead.
#> ℹ Set `bins` argument to enable binning.