scandal_cell_complexity_distribution_plot: Complexity distribution plot

In dravishays/scandal: A framework for single-cell analysis

Description

Computes the complexity (number of genes with expression > 0) of each cell in x and plots the distribution using a scatter plot. Adds two horizontal lines demarcating the lower and upper bounds of *complexity cutoff* parameter.

Usage

scandal_cell_complexity_distribution_plot(
  x,
  complexity_cutoff,
  sample_id,
  project_id = ".",
  show_plot = TRUE,
  save_to_file = TRUE
)

Arguments

x	an expression matrix.
complexity_cutoff	a numeric vector of length 2 representing the lower and upper bounds of complexity (i.e. the number of detected genes per cell).
sample_id	an ID of the sample being processed. Used for generating the filename and hence is mandatory.
project_id	a character identifier of the current project. Used for saving generated plot to the project's plots directory. Default is "." (current working directory).
show_plot	logical indicating if the plots should be printed to the graphics device. Allows saving the plots without printing to the graphics device by setting to FALSE. Default is TRUE.
save_to_file	logical indicating wether the plots should be saved to the plots directory. Default is TRUE.

Value

Invisibly returns the generated plot.

Author(s)

Avishay Spitzer

See Also

scandal_scatter_plot, compute_complexity

dravishays/scandal documentation built on Jan. 8, 2020, 1:30 p.m.