make_bioscope_plot {ceas}

Bioenergetic Scope Plot Shortcut

Description

Wrapper to create a 2D plot visualizing the mean and standard deviation basal and maximal ATP production from glycolysis and OXPHOS for each experimental group Create a Bioenergetic scope plot from input Seahorse Wave export, long-form rates excel files

Usage

make_bioscope_plot(rep_list, ph, pka, buffer, sheet = 2)

Arguments

rep_list

A list of Seahorse Wave excel export files. One file per replicate. Group all replicates for a given experiment in a single folder, and write that folder's path in "seahorse_data". You can use 'list.files("seahorse_data") "full.names=TRUE") to get the paths to the files.

ph

pH value for energetics calculation (for XF Media, 7.5)

pka

pKa value for energetics calculation (for XF Media, 6.063)

buffer

buffer for energetics calculation (for XF Media, 0.1 mpH/pmol H+)

sheet

The number of the excel sheet containing the long-form Seahorse data. Default is 2 because the long-form output from Seahorse Wave is on sheet 2

Value

a ggplot

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
make_bioscope_plot(rep_list, ph = 7.4, pka = 6.093, buffer = 0.1)