atp_plot {ceas}

ATP Plot

Description

Generate the ATP Plot

Usage

atp_plot(
  energetics,
  error_bar = "ci",
  conf_int = 0.95,
  size = 2,
  shape = 21,
  basal_vs_max = "basal",
  glyc_vs_resp = "glyc",
  group_label = "Experimental group"
)

Arguments

energetics

A table of calculated glycolysis and OXPHOS rates. Returned by get_energetics

error_bar

Whether to plot error bars as standard deviation ("sd") or confidence intervals ("ci")

conf_int

The confidence interval percentage. Should be between 0 and 1

size

Size of the points

shape

Shape of the points

basal_vs_max

Whether to plot "basal" or "max" respiration

glyc_vs_resp

Whether to plot glycolysis ("glyc") or respiration ("resp")

group_label

Label for the experimental group to populate the legend title

Details

Note: When we use the term 'max' in the package documentation we mean the maximal experimental OCR and ECAR values rather than absolute biological maximums.

Value

a ggplot

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
seahorse_rates <- read_data(rep_list, sheet = 2)
partitioned_data <- partition_data(seahorse_rates)
energetics <- get_energetics(partitioned_data, ph = 7.4, pka = 6.093, buffer = 0.1)
atp_plot(energetics)

atp_plot(energetics, basal_vs_max = "max")

atp_plot(energetics, basal_vs_max = "basal", glyc_vs_resp = "resp")

# to change fill, the geom_point shape number should be between 15 and 25
atp_plot(energetics, shape = 21) + # filled circle
  ggplot2::scale_fill_manual(values = c("#e36500", "#b52356", "#3cb62d", "#328fe1"))

# to change color, use ggplot2::scale_color_manual
atp_plot(energetics) +
  ggplot2::scale_color_manual(values = c("#e36500", "#b52356", "#3cb62d", "#328fe1"))