Plot frequency polygons for colData and rowData columns
Source:R/plot-non-spatial.R
plotColDataFreqpoly.Rd
This function is recommended instead of plotColDataHistogram
when coloring by multiple categories and log transforming the y axis, which
causes problems in stacked histograms.
Usage
plotColDataFreqpoly(
sce,
feature,
color_by = NULL,
subset = NULL,
bins = 100,
binwidth = NULL,
linewidth = 1.2,
scales = "free",
ncol = 1,
position = "identity"
)
plotRowDataFreqpoly(
sce,
feature,
color_by = NULL,
subset = NULL,
bins = 100,
binwidth = NULL,
linewidth = 1.2,
scales = "free",
ncol = 1,
position = "identity"
)
Arguments
- sce
A
SingleCellExperiment
object.- feature
Names of columns in
colData
orrowData
to plot. When multiple features are specified, they will be plotted in separate facets.- color_by
Name of a categorical column in
colData
orrowData
to color the polygons.- subset
Name of a logical column to only plot a subset of the data.
- bins
Number of bins. Overridden by
binwidth
. Defaults to 30.- 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.
- linewidth
Line width of the polygons, defaults to a thicker 1.2.
- 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 useposition_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.
Examples
library(SFEData)
sfe <- McKellarMuscleData()
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
plotColDataFreqpoly(sfe, c("nCounts", "nGenes"), color_by = "in_tissue",
bins = 50)
plotColDataFreqpoly(sfe, "nCounts", subset = "in_tissue")
sfe2 <- sfe[, sfe$in_tissue]
plotColDataFreqpoly(sfe2, c("nCounts", "nGenes"), bins = 50)