plot() creates a plot depicting the current state of a sceptre_object.
Usage
# S4 method for sceptre_object
plot(x, y, ...)Arguments
- x
a
sceptre_object- y
ignored argument
- ...
arguments passed to the plotting function dispatched by
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)
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().
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()