Plot and compare action potential parameters before and after a treatment

Usage

plot_AP_comparison(
  data,
  plot_treatment = "Control",
  plot_category = 2,
  baseline_label = "Baseline",
  post_hormone_label = "Post-hormone",
  y_variable,
  y_axis_title,
  test_type,
  treatment_colour_theme,
  theme_options,
  save_plot_png = "no",
  ggplot_theme = patchclampplotteR_theme()
)

Arguments

data: The action potential data generated from add_new_cells() with data_type == "AP".
plot_treatment: A character value specifying the treatment you would like to plot (e.g. "Control"). plot_treatment represents antagonists that were present on the brain slice, or the animals were fasted, etc.
plot_category: A numeric value specifying the category, which can be used to differentiate different protocol types. In the sample dataset for this package, plot_category == 2 represents experiments where insulin was applied continuously after a 5-minute baseline period.
baseline_label: A character value for the x-axis label applied to the pre-hormone state. Defaults to "Baseline".
post_hormone_label: A character value for x-axis label applied to the post-hormone or post-protocol state. Defaults to "Post-hormone" but you will likely change this to the hormone or protocol name.
y_variable: A character value naming the variable to be plotted on the y-axis. Must be a column present in data. Examples include peak_amplitude, time_to_peak, antipeak_amplitude and half_width.
y_axis_title: A character value used to define a "pretty" version of y_variable. This will become the y-axis label on the ggplot. Examples include "Peak Amplitude (pA)" or "Time to Peak (ms)".
test_type: A character (must be "wilcox.test", "t.test" or "none") describing the statistical model used to create a significance bracket comparing the pre- and post-hormone groups.
treatment_colour_theme: A dataframe containing treatment names and their associated colours as hex values. See sample_treatment_names_and_colours for an example of what this dataframe should look like.
theme_options: A dataframe containing theme options. See sample_theme_options for an example of what this dataframe should look like.
save_plot_png: A character ("yes" or "no"). If "yes", the plot will be saved as a .png using ggsave. The filepath depends on the current type, but they will all go in subfolders below Figures/ in your project directory.
ggplot_theme: The name of a ggplot theme or your custom theme. This will be added as a layer to a ggplot object. The default is patchclampplotteR_theme(), but other valid entries include theme_bw(), theme_classic() or the name of a custom ggplot theme stored as an object.

Value

A ggplot object. If save_plot_png == "yes", it will also generate a .png file in the folder Figures/Action-potentials relative to the project directory. The treatment and y_variable will be included in the filename.

Examples

plot_AP_comparison(
  sample_AP_data,
  plot_treatment = "Control",
  plot_category = 2,
  y_variable = "peak_amplitude",
  y_axis_title = "Peak Amplitude (pA)",
  theme_options = sample_theme_options,
  baseline_label = "Baseline",
  test_type = "wilcox.test",
  post_hormone_label = "Insulin",
  treatment_colour_theme = sample_treatment_names_and_colours,
  save_plot_png = "no"
)