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 for EPSC summary plots

Plot data

Functions to plot the data.

plot_raw_current_data(): Make raw current plots

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

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

plot_PPR_data_multiple_treatments(): Make a PPR plot for multiple treatments

plot_baseline_data(): Make baseline comparison plot

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

plot_variance_comparison_data(): Plot variance comparison for a treatment

plot_spontaneous_current_parameter_comparison(): Visually compare spontaneous current parameters

plot_spontaneous_current_trace(): Plot a representative spontaneous current trace

patchclampplotteR_theme(): Add a customized ggplot2 theme

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