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Plot histograms for colData and rowData columns

Source: R/plot-non-spatial.R
plotColDataHistogram.Rd

Plot histograms for colData and rowData columns

Usage

plotColDataHistogram(
  sce,
  feature,
  fill_by = NULL,
  facet_by = NULL,
  subset = NULL,
  bins = 100,
  binwidth = NULL,
  scales = "free",
  ncol = 1,
  position = "stack",
  ...
)

plotRowDataHistogram(
  sce,
  feature,
  fill_by = NULL,
  facet_by = NULL,
  subset = NULL,
  bins = 100,
  binwidth = NULL,
  scales = "free",
  ncol = 1,
  position = "stack",
  ...
)

Arguments

sce

A SingleCellExperiment object.

feature

Names of columns in colData or rowData to plot. When multiple features are specified, they will be plotted in separate facets.

fill_by

Name of a categorical column in colData or rowData to fill the histogram.

facet_by

Column in colData or rowData to facet with. When multiple features are plotted, the features will be in different facets. In this case, setting facet_by will call facet_grid so the features are in rows and categories in facet_by will be in columns.

subset

Name of a logical column to only plot a subset of the data.

bins

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

binwidth

The width of the bins. Can be specified as a numeric value or as a function that calculates width from unscaled x. Here, "unscaled x" refers to the original x values in the data, before application of any scale transformation. When specifying a function along with a grouping structure, the function will be called once per group. The default is to use the number of bins in bins, covering the range of the data. You should always override this value, exploring multiple widths to find the best to illustrate the stories in your data.

The bin width of a date variable is the number of days in each time; the bin width of a time variable is the number of seconds.

scales

Should scales be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_x", "free_y")?

ncol

Number of columns in the facetting.

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

...

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

See also

plotColDataFreqpoly

Examples

library(SFEData)
sfe <- McKellarMuscleData()
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
plotColDataHistogram(sfe, c("nCounts", "nGenes"), fill_by = "in_tissue",
                     bins = 50, position = "stack")

plotColDataHistogram(sfe, "nCounts", subset = "in_tissue")

sfe2 <- sfe[, sfe$in_tissue]
plotColDataHistogram(sfe2, c("nCounts", "nGenes"), bins = 50)