plot_density: Density ridges for two sets

In biosurf/cyCombine: Robust integration of single-cell cytometry datasets within and across technologies

Density ridges for two sets

Description

Compare densities between each batch both before and after correction. Thanks to GitHub user asongggg for suggesting storing markers on separate pages and for suggesting an approach.

Usage

plot_density(
  uncorrected,
  corrected,
  markers = NULL,
  directory = NULL,
  filename = NULL,
  y = "batch",
  dataset_names = NULL,
  xlims = c(-1, 10),
  ncol = 6,
  format = 1,
  markers_per_page = NULL,
  return_format = c("cowplot", "raw", "pdf")
)

Arguments

uncorrected	tibble with uncorrected data
corrected	tibble with corrected data
markers	Character vector with the markers to plot
directory	Folder to store figures in.
filename	Output figure filename. If NULL plots are returned
y	The column to stack densities with. Default: "batch". If set to "Type", the dataset_names will be used to stack densities.
dataset_names	Change the names of the datasets from Uncorrected and Corrected to something else. Format: c("Uncorrected", "Corrected")
xlims	The limits of the x axis as a vector
ncol	Number of density plots in a single row of plots. Default: 6
format	Plotting format (1 = 1 row per batch, 2 = all batches in same row.)
markers_per_page	Store figures on individual pages, with the number of markers as specified. Default: NULL.
return_format	Allows returning the raw plots for manual adjustments. This argument is mainly used when plots are not stored in files.

See Also

Other plot: plot_dimred(), plot_dimred_full(), plot_save_four(), plot_save_two(), plot_umap_labels()

Examples

## Not run: 
plot_density(uncorrected, corrected, y = 'batch', filename = 'my/dir/batchcor_plot.pdf')
plot_density(imputed1, imputed2, y = 'Type', dataset_names = paste('Panel', 1:2),
             filename = 'my/dir/merging_plot.pdf')

## End(Not run)

biosurf/cyCombine documentation built on May 23, 2024, 4:07 a.m.