Package index • patchclampplotteR

Import data

Functions that import raw data (typically as a comma-separated file (.csv) or Axon Binary Format (.abf) file).

import_ABF_file(): Import raw .abf files as a dataframe

import_cell_characteristics_df(): Import cell characteristics

import_theme_colours(): Import colour theme

import_ext_data(): Get path to external data for package examples

add_new_cells(): Add new data

Modify data

Functions that normalize, prune, and summarize the data.

make_normalized_EPSC_data(): Import and normalize raw current data

make_pruned_EPSC_data(): Prune and summarize raw current data per minute

make_summary_EPSC_data(): Summarize current data per 5-min for statistical tests

make_PPR_data(): Make paired-pulse ratio (PPR) dataframe for before vs. after comparisons

make_variance_data(): Make dataframe with variance measures

make_interactive_summary_table(): Make interactive overview table of all recordings

perform_t_tests_for_summary_plot(): Perform t-tests (or Wilcoxon tests) for EPSC summary plots

Plot data

Functions to plot the data.

patchclampplotteR_theme(): Add a customized ggplot2 theme

insert_png_as_ggplot(): Import an image as a ggplot object

plot_cell_coordinates_data(): Plot cell location data

Evoked and spontaneous currents

plot_raw_current_data(): Make raw current plots

plot_summary_current_data(): Make a summary plot for a specific treatment

plot_baseline_data(): Make baseline comparison plot

plot_percent_change_comparisons(): Plot percent change comparisons

Spontaneous currents only

plot_spontaneous_current_parameter_comparison(): Visually compare spontaneous current parameters

plot_spontaneous_current_trace(): Plot a representative spontaneous current trace

Paired-pulse ratio

plot_PPR_data_single_treatment(): Make a PPR plot for a single treatment

plot_PPR_data_multiple_treatments(): Make a PPR plot for multiple treatments

Action potentials

plot_AP_trace(): Plot action potential recording

plot_AP_comparison(): Plot and compare action potential parameters before and after a treatment

plot_AP_frequencies_single_treatment(): Plot action potential frequency curves for a single treatment

plot_AP_frequencies_multiple_treatments(): Plot action potential frequency curves for multiple treatments

Variance analysis

plot_cv_data(): Make a plot of coefficient of variation over time

plot_variance_comparison_data(): Plot variance comparison for a treatment

Sample datasets

Sample datasets for vignettes and examples.

sample_cell_characteristics: Information about sex, age, treatment, and animal ID

sample_abf_file: Evoked current recording excerpt

sample_theme_options: A dataframe of theme options for things like colours and line widths

sample_treatment_names_and_colours: A dataframe of treatments and their assigned colours for consistency across plots

Evoked current (eEPSC) data

Sample datasets from recordings measuring evoked current amplitude over time. The paired-pulse ratio (PPR) data are only available for evoked current recordings because the PPR is determined from evoked current amplitudes, not spontaneous currents.

sample_raw_eEPSC_df: Representative data from a series of evoked (eEPSC) currents

sample_pruned_eEPSC_df: Evoked current data pruned to a summary point per minute

sample_summary_eEPSC_df: Evoked current data summarized into 5-minute intervals

sample_eEPSC_variance_df: Variance-to-mean ratio and coefficient of variation of evoked current amplitudes

sample_PPR_df: Evoked current data filtered to focus on paired-pulse ratio (PPR) analysis

sample_eEPSC_t_test_df: Paired t-test results comparing evoked current amplitudes relative to baseline

Spontaneous current (sEPSC) data

Sample datasets from recordings measuring spontaneous current amplitude over time. To reduce package size, only the raw and pruned spontaneous current data are included.

sample_raw_sEPSC_df: Representative data from a series of spontaneous (sEPSC) currents

sample_pruned_sEPSC_df: Spontaneous current data pruned to a summary point per minute

sample_summary_sEPSC_df: Spontaneous current data summarized into 5-minute intervals

sample_sEPSC_t_test_df: Paired t-test results comparing spontaneous current amplitudes relative to baseline amplitudes

Action Potential (AP) data

Sample datasets from recordings measuring action potentials in response to a current injection protocol.

sample_AP_data: Example of a complete action potential dataset used for plotting and analyses. This data contains parameters like peak_amplitude, after-hyperpolarization amplitude, and half-width for two time-points: during the control period (state == "Baseline") or after insulin has been applied (state == "Insulin").

sample_AP_count_data: Example of action potential count data for two time-points: during the control period (state == "Baseline") or after insulin has been applied (state == "Insulin"). These were obtained by counting the number of action potentials present within each sweep. The data were then merged with the sample_cell_characteristics data through add_new_cells() with data_type = "AP_count".

sample_ap_abf_baseline: Action potential baseline recording