scandal_mean_housekeeping_expression_plot: Housekeeping genes expression plot

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

Description

Computes the *log2(mean expression)* of housekeeping genes for each cell in x and plots the distribution using a scatter plot. Adds a horizontal line demarcating the *housekeeping cutoff* parameter.

Usage

scandal_mean_housekeeping_expression_plot(
  x,
  housekeeping_cutoff,
  sample_id,
  project_id = ".",
  show_plot = TRUE,
  save_to_file = TRUE
)

Arguments

x	an expression matrix.
housekeeping_cutoff	a numeric representing the log2 mean expression of house-keeping genes (i.e. genes that are highly expressed in all cells) per cell below which a cell is considered low quality.
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, SCANDAL_HOUSEKEEPING_GENES_LIST

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