plot_assign_grnas: Plot assign gRNAs

In timothy-barry/sceptre: Analysis of Single-Cell CRISPR Screen Data

Plot assign gRNAs

Description

plot_assign_grnas() plots the outcome of the gRNA-to-cell assignment step. The top panel plots the gRNA-to-cell assignments of n_grnas_to_plot (default 3) randomly selected gRNAs. In each plot the points represent cells; the vertical axis indicates the UMI count of the gRNA in a given cell, and the horizontal axis indicates whether the cell has been classified as “perturbed” (i.e., it contains the gRNA) or unperturbed (i.e., it does not contain the gRNA). Perturbed (resp., unperturbed) cells are shown in the left (resp., right) column. The bottom left panel is a barplot of the number of cells to which each gRNA has been mapped. Finally, the bottom right panel is a histogram of the number of gRNAs contained in each cell. The mean number of gRNAs per cell — i.e., the MOI — is displayed in purple text.

Usage

plot_assign_grnas(
  sceptre_object,
  n_grnas_to_plot = 3L,
  grnas_to_plot = NULL,
  point_size = 0.9,
  transparency = 0.8,
  return_indiv_plots = FALSE
)

Arguments

sceptre_object	a sceptre_object that has had assign_grnas() called on it
n_grnas_to_plot	(optional; default 3) the number of gRNAs to display in the plots of gRNA count versus cell assignment
grnas_to_plot	(optional; default NULL) a character vector giving the names of specific gRNAs to plot; if NULL, then the gRNAs are chosen at random.
point_size	(optional; default 0.9) the size of the individual points in the plot
transparency	(optional; default 0.8) the transparency of the individual points in the plot
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)

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
) |>
  set_analysis_parameters() |>
  assign_grnas(method = "thresholding") |>
  plot_assign_grnas()

timothy-barry/sceptre documentation built on Nov. 19, 2024, 10:04 a.m.