scandal_plot_qc_metrics: Plot quality control metrics

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

Description

This function generates 3 types of plots for each node in object:

1. A scatter plot depicting the distribution of complexities within each node.

2. A scatter plot depicting the mean expression of housekeeping gene for each cell.

3. A hostogram plot depicting the mean expression distribution of each gene.

The function is inteneded to be called **prior** to preproccesing to assist in choosing the right QC thresholds for each metric and enable plotting and saving in bulk for all the nodes contained in object.

Usage

scandal_plot_qc_metrics(
  object,
  show_plot = TRUE,
  save_to_file = TRUE,
  histogram_bin_width = 0.2
)

Arguments

object	a ScandalDataSet object.
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.
histogram_bin_width	controls the width of each histogram bin. Default is 0.2.

Author(s)

Avishay Spitzer

See Also

plot_cell_complexity_distribution, plot_mean_housekeeping_expression, plot_mean_expression_frequency

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