Welcome to pastaWRAP!

pastaWRAP is a Python wrapper for R-based Awesome Toolkit for PASTA, more commonly known as ratPASTA - an R package used for processing and visualising data from startle experiments in rodents or experiments measuring grip strength in rodents. Currently, pastaWRAP only supports ratPASTA functionality for startle experiments, with plans for adding griPASTA (grip strength test) functionality wrapping at a later date. The input data for this package is created with a PASTA solution (Platform for Acoustic STArtle), described in detail here:

Virag, D., Homolak, J., Kodvanj, I., Babic Perhoc, A., Knezovic, A., Osmanovic Barilar, J., & Salkovic-Petrisic, M. (2020). Repurposing a digital kitchen scale for neuroscience research: a complete hardware and software cookbook for PASTA. BioRxiv, 2020.04.10.035766. https://doi.org/10.1101/2020.04.10.035766

Using the same platform for measuring grip strength in rodents is described here:

Homolak, J., Virag, D., Kodvanj, I., Matak, I., Babic Perhoc, A., Knezovic, A., Osmanovic Barilar, J., Salkovic-Petrisic, M. (2020). griPASTA: A hacked kitchen scale for quantification of grip strength in rodents. BioRxiv, 2020.07.23.217737. https://doi.org/10.1101/2020.07.23.217737

Full pastaWRAP source code is available here under the GPLv3 license.


Documentation

class pastawrap.RatPasta(*args, **kwargs)

The RatPasta class used for wrapping the ratPASTA functionality of the ratPASTA R package.

This is a Python class which wraps all ratPASTA R functionality. When instantiated, all parameters are passed to the load_startle_data() method, which stores the working data as an R dataframe in self.df. The class also stores its methods’ outputs into appropriate attributes, listed below. The last generated plot is stored in self.last_plot. All plots may be modified by appending rpy2.robjects.lib.ggplot2 functions’ outputs to them using the ‘+’ operator (for more information on available parameters, please see rpy2’s ggplot2 library documentation). All parameters are passed to the load_startle_data() method’s R function - only some are explained here. For more information, please refer to ratPASTA documentation.

Parameters

  • addhead (float) – Correction factor for the animal’s latency (before the pulse).

  • addtail (float) – Correction factor for the animal’s latency (after the pulse).

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

  • *args – Arguments, passed verbatim to the load_startle_data() method.

  • **kwargs – Keyword arguments, passed verbatim to the load_startle_data() method.

Variables

  • df (rpy2.robjects.vectors.DataFrame) – R dataframe of raw .pasta data imported using load_startle_data(), passed by default to the summary and plotting methods.

  • summary (dict of pandas.core.frame.DataFrame) – A dictionary containing three pandas dataframes: “values”, “ratio” and “ratio_s”, automatically (re)generated on every data load.

  • plots (nested dict of rpy2.robjects.lib.ggplot2.GGPlot) – A dictionary containing plots generated by the last invocation of each of the plotting methods. Unlike “basic_startle_plot” and “startle_plot” keys in this dict which contain a ggplot, the “latency_plot” key is a nested dictionary containing latency_vs_cycle and latency_vs_group keys, which contain the corresponding latency plots. All values default to None if the respective method hasn’t been invoked yet.

  • last_plot (rpy2.robjects.lib.ggplot2.GGPlot) – Contains the last generated plot by any of the plotting methods.

>>> rp = pastawrap.RatPasta(addhead=0.5, addtail=0.5)

>>> rp.startle_plot(type=2)
>>> import rpy2.robjects.lib.ggplot2 as ggplot2
>>> rp.last_plot += ggplot2.theme_light()
basic_startle_plot(df=None, *args, **kwargs)

Plotting method. Calls ratPASTA’s basicStartlePlot()

All parameters are passed to the respective R function. For more information, please refer to ratPASTA documentation.

Parameters

  • df – R dataframe to be plotted, defaults to self.df (auto-generated using load_startle_data() when instantiating the RatPasta class)

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

A ggplot, which is also stored in self.plots and self.last_plot.

Return type

rpy2.robjects.lib.ggplot2.GGPlot

latency_plot(df=None, *args, **kwargs)

Plotting method. Calls ratPASTA’s latencyPlot()

All parameters are passed to the respective R function. For more information, please refer to ratPASTA documentation.

Parameters

  • df (rpy2.robjects.vectors.DataFrame) – R dataframe to be plotted, defaults to self.df (auto-generated using load_startle_data() when instantiating the RatPasta class)

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

A dict containing two ggplots: latency_vs_cycle and latency_vs_group

Return type

dict of rpy2.robjects.lib.ggplot2.GGPlot

load_startle_data(*args, **kwargs)

Load startle data. Calls ratPASTA’s loadStartleData()

Clears all instance attributes on load and regenerates self.summary so as to avoid confusing freshly loaded data with plots and summaries of old data. All parameters are passed to the respective R function - only some are explained here. For more information, please refer to ratPASTA documentation.

Parameters

  • addhead (float) – Correction factor for the animal’s latency (before the pulse).

  • addtail (float) – Correction factor for the animal’s latency (after the pulse).

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

R dataframe which can be passed to pastaWRAP plotting methods.

Return type

rpy2.robjects.vectors.DataFrame

plot_close()

Closes the ggplot2 plotting window.

plot_save(plot=None, plot_key=None, *args, **kwargs)

Saves a plot using ggsave.

Saves the last plot generated, or the one specified by plot, using the ggsave wrapper function, r_ggsave(). For more information, please refer to ggplot2’s ggsave documentation.

Parameters

plot (str) – Plot to save, defaults to the last generated plot (self.last_plot).

Returns

None

>>> rp.plot_save(filename="test.png", width=10, height=8, dpi=150, units="in", device="png")
plot_show(plot_key=None)

Shows the ggplot2 plotting window.

Displays the last plot generated (stored in self.last_plot) in a ggplot2 plotting window.

Parameters

plot_key (str) – Currently only used when displaying a latency plot, in which case it can be either latency_vs_cycle or latency_vs_group, defaults to None.

Returns

None

>>> rp.plot_show() # usual usage
>>> rp.plot_show(plot_key="latency_vs_group") # for latency plots
startle_plot(df=None, type=None, *args, **kwargs)

Plotting method. Calls ratPASTA’s startlePlot()

All parameters are passed to the respective R function. For more information, please refer to ratPASTA documentation.

Parameters

  • df (rpy2.robjects.vectors.DataFrame) – R dataframe to be plotted, defaults to self.df (auto-generated using load_startle_data() when instantiating the RatPasta class)

  • type (int) – Type of startle plot. Please refer to ratPASTA documentation for available types.

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

A ggplot, which is also stored in self.plots and self.last_plot.

Return type

rpy2.robjects.lib.ggplot2.GGPlot

summarise_startle(df=None, *args, **kwargs)

Generate a summary. Calls ratPASTA’s summariseStartle()

All parameters are passed to the respective R function. For more information, please refer to ratPASTA documentation.

Parameters

  • df – R dataframe to be processed, defaults to self.df (auto-generated using load_startle_data() when instantiating the RatPasta class)

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

A dictionary containing three pandas dataframes: values, ratio and ratio_s, which is also stored in self.summary.

Return type

dict of pandas.core.frame.DataFrame

pastawrap.r_ggsave(*args, **kwargs)

A wrapper for R ggplot2’s ggsave function.

All parameters are passed to the respective R function. For more information, please refer to the ggplot2 documentation.

Parameters

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

None

pastawrap.r_install_packages(package)

A wrapper for R utils install.packages function.

All parameters are passed to the respective R function. For more information, please refer to the R utils documentation.

Parameters

  • *args – Arguments, passed verbatim to the respective R function.

  • **kwargs – Keyword arguments, passed verbatim to the respective R function.

Returns

None


Indices and tables