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patchclampplotteR

patchclampplotteR provides a set of user-friendly tools for electrophysiologists who want to plot and analyze data from whole-cell patch clamp electrophysiology recordings. Here’s some of the functions that this package can do (see below for examples!):

A banner with pictures of some of the plots that can be created with the patchclampplotteR package.

  • Plot raw evoked or spontaneous current amplitudes over time for all recordings at once.
  • Normalize current amplitudes relative to mean baseline values.
  • Plot normalized current amplitudes over time for all recordings.
  • Plot summary data for a specific treatment, grouped by sex.
  • Plot representative spontaneous current traces from an .abf file with a scale bar.
  • Compare spontaneous current amplitude and frequency
  • Compare variance parameters to help determine presynaptic mechanisms.
  • And more!

Examples

Plot raw evoked currents for a specific cell:

raw_eEPSC_control_plots <- plot_raw_current_data(
  data = sample_raw_eEPSC_df,
  plot_treatment = "Control",
  plot_category = 2,
  current_type = "eEPSC",
  y_variable = "P1",
  pruned = "no",
  hormone_added = "Insulin",
  hormone_or_HFS_start_time = 5,
  theme_options = sample_theme_options,
  treatment_colour_theme = sample_treatment_names_and_colours
)

raw_eEPSC_control_plots$AO

A plot of evoked current amplitude (in pA) over time in minutes showing a decrease in evoked current amplitude after adding insulin.

Plot evoked current amplitudes summarized by sex:

plot_summary_current_data(
  plot_category = 2,
  plot_treatment = "Control",
  data = sample_pruned_eEPSC_df$all_cells,
  current_type = "eEPSC",
  y_variable = "amplitude",
  include_representative_trace = "no",
  y_axis_limit = 175,
  signif_stars = "yes",
  t_test_df = sample_eEPSC_t_test_df,
  hormone_added = "Insulin",
  large_axis_text = "no",
  shade_intervals = "no",
  hormone_or_HFS_start_time = 5,
  treatment_colour_theme = sample_treatment_names_and_colours,
  theme_options = sample_theme_options
)

A scatterplot showing evoked current amplitude (% baseline) versus time in minutes, where 500 nM of insulin have been added from 5 minutes and onwards. Insulin significantly decreased current amplitude in both males and females.

Plot a representative recording trace showing spontaneous currents from a raw Axon Binary File (.ABF):

plot_spontaneous_current_trace(
  file = sample_abf_file,
  plot_colour = "#6600cc",
  include_scale_bar = "yes",
  plot_episode = "epi1",
  scale_bar_x_length = 1,
  scale_bar_y_length = 10,
  plot_x_min = 1,
  plot_x_max = 3
)

A representative trace from a raw abf recording, showing a series of noisy, negative-going peaks. Each peak represents a spontaneous current

Installation

You can install the development version of patchclampplotteR from GitHub with:

# install.packages("pak")
pak::pak("christelinda-laureijs/patchclampplotteR")

And then load the package with library():

Analysis

To learn about how to convert raw .abf data in Clampfit to .csv files for this package, please see the vignettes Evoked Current Analysis and Action Potential Analysis.

Using patchclampplotteR

Please see the Getting Started page for a walk-through of the major functions of this package.