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Plot covariates

Source: R/plotting_functions.R
plot_covariates.Rd

plot_covariates() creates a histogram of the covariates response_n_nonzero, response_n_umis, and (if applicable) response_p_mito. Cellwise QC removes cells that lie in the extreme right tail of the response_p_mito distribution or that lie in the extreme left or right tail of the response_n_nonzero or response_n_umis distribution. To help guide the selection of QC thresholds, plot_covariates() plots candidate QC thresholds as vertical lines on the histograms. The optional arguments response_n_nonzero_range, response_n_umis_range, and p_mito_threshold control the location of these candidate QC thresholds. response_n_nonzero_range (resp., response_n_umis_range) is a length-two vector of quantiles (default: c(0.01, 0.99)) indicating the location at which to draw candidate QC thresholds on the response_n_nonzero (resp., response_n_umis) histogram. Next, p_mito_threshold is a single numeric value in the interval [0,1] specifying the location at which to draw a candidate QC threshold on the response_p_mito plot.

Usage

plot_covariates(
  sceptre_object,
  response_n_umis_range = c(0.01, 0.99),
  response_n_nonzero_range = c(0.01, 0.99),
  p_mito_threshold = 0.2,
  return_indiv_plots = FALSE
)

Arguments

sceptre_object

a sceptre_object

response_n_umis_range

(optional; default c(0.01, 0.99)) a length-2 vector of quantiles indicating the location at which to draw vertical lines on the response_n_umis histogram

response_n_nonzero_range

(optional; default c(0.01, 0.99)) a length-2 vector of quantiles indicating the location at which to draw vertical lines on the response_n_nonzero histogram

p_mito_threshold

(optional; default 0.2) a single numeric value in the interval [0,1] specifying the location at which to draw a vertical line on the response_p_mito histogram. Note that p_mito_threshold is an absolute number rather than a percentile.

return_indiv_plots

(optional; default FALSE) if FALSE, then a list of ggplot objects is returned; if TRUE then a single cowplot object is returned.

Value

a single cowplot object containing the combined panels (if return_indiv_plots is set to TRUE) or a list of the individual panels (if return_indiv_plots is set to FALSE)

Note

If run_qc() has already been called on the sceptre_object, then the parameters response_n_umis_range, response_n_nonzero_range, and p_mito_threshold are set to the corresponding parameters within the sceptre_object.

Examples

library(sceptredata)
data(highmoi_example_data)
data(grna_target_data_frame_highmoi)
import_data(
  response_matrix = highmoi_example_data$response_matrix,
  grna_matrix = highmoi_example_data$grna_matrix,
  grna_target_data_frame = grna_target_data_frame_highmoi,
  moi = "high",
  extra_covariates = highmoi_example_data$extra_covariates,
  response_names = highmoi_example_data$gene_names
) |> plot_covariates(p_mito_threshold = 0.07)