plot-sceptre_object-method: Plot

In Katsevich-Lab/sceptre: Analysis of Single-Cell CRISPR Screen Data

Plot

Description

plot() creates a plot depicting the current state of a sceptre_object.

Usage

## S4 method for signature 'sceptre_object'
plot(x, y, ...)

Arguments

x	a sceptre_object
y	ignored argument
...	arguments passed to the plotting function dispatched by plot()

Details

plot() is "generic" in the sense that it dispatches a specific plotting function based on the pipeline function that was most recently called on the sceptre_object. For example, if run_assign_grnas() is the most recently called pipeline function, then plot() dispatches plot_run_assign_grnas(). Similarly, if run_power_check() is the most recently called pipeline function, then plot() dispatches plot_run_power_check(), and so on. Users can pass arguments to the function dispatched by plot() as named arguments to plot().

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
sceptre_object <- 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
sceptre_object <- sceptre_object |>
  set_analysis_parameters() |>
  assign_grnas(method = "thresholding") |>
  plot()

Katsevich-Lab/sceptre documentation built on Nov. 19, 2024, 5:16 p.m.