Make interactive overview table of all recordings — make_interactive_summary

This function pulls information from multiple dataframes to display everything about a cell (cell characteristics, evoked current data, and spontaneous current data) in an interactive table. The table is made with reactable::reactable(), so it can be filtered, sorted, and rearranged.

Usage

make_interactive_summary_table(
  cell_characteristics_dataframe,
  pruned_eEPSC_dataframe,
  pruned_sEPSC_dataframe,
  treatment_colour_theme,
  include_all_treatments = "yes",
  list_of_treatments = NULL,
  include_all_categories = "yes",
  list_of_categories = NULL,
  save_output_as_RDS = "no",
  ggplot_theme = patchclampplotteR_theme()
)

Arguments

cell_characteristics_dataframe: A dataframe containing the cell characteristics, generated from import_cell_characteristics_df().
pruned_eEPSC_dataframe: A dataframe containing pruned evoked current data, generated from make_pruned_EPSC_data(), where current_type == "eEPSC".
pruned_sEPSC_dataframe: A dataframe containing pruned spontaneous current data, generated from make_pruned_EPSC_data(), where current_type == "sEPSC".
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.
include_all_treatments: A character ("yes" or "no") specifying if the plot will include data from all treatments. If "no", you must specify a list of treatments in list_of_treatments.
list_of_treatments: A list of character values describing the treatments that will be in the plot. Defaults to NULL, since include_all_treatments is "yes" by default.
include_all_categories: A character ("yes" or "no") specifying if the plot will include data from all categories. If "no", you must specify a list of categories in list_of_categories.
list_of_categories: A list of character values describing the categories that will be in the plot. Defaults to NULL, since include_all_categories is "yes" by default.
save_output_as_RDS: A character ("yes" or "no") describing if the resulting object should be saved as an RDS file in the folder "Data/Output-Data-from-R". The function will automatically create this folder if it doesn't already exist. Note: This is not the interactive table, but it is the raw dataframe that is later inserted into reactable::reactable(). This is useful if you want to build your own table using a different package, or you want to generate a customized reactable table yourself.
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 reactable HTML widget that can be viewed in RStudio or exported in RMarkdown HTML documents. If save_output_as_RDS == "yes", the raw dataframe used to create the reactable is also exported as an .rds file into Data/Output-Data-from-R/.

Details

The table contains sparklines of the evoked current and spontaneous current amplitudes over time, which allows you to visually compare the overall response of a group of cells.

The sparklines are colour-coded by treatment, allowing you to quickly identify trends in response to a hormone/protocol for all cells belonging to a particular treatment.

Examples


# Note, the number of treatments is limited to "Control" and "PPP" to reduce run-time
make_interactive_summary_table(
  cell_characteristics_dataframe = sample_cell_characteristics,
  pruned_eEPSC_dataframe = sample_pruned_eEPSC_df,
  pruned_sEPSC_dataframe = sample_pruned_sEPSC_df,
  treatment_colour_theme = sample_treatment_names_and_colours,
  include_all_treatments = "no",
  list_of_treatments = c("Control", "PPP"),
  include_all_categories = "yes",
  list_of_categories = NULL,
  save_output_as_RDS = "no"
)