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ATP Plot

Source: R/atp_plot.R
atp_plot.Rd

Generate the ATP Plot

Usage

atp_plot(
  energetics,
  model = "ols",
  error_bar = "ci",
  conf_int = 0.95,
  size = 2,
  shape = 16,
  basal_vs_max = "basal",
  glyc_vs_resp = "glyc",
  group_label = "Experimental group",
  sep_reps = FALSE,
  ci_method = "Wald"
)

Arguments

energetics

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

model

The linear model used to estimate mean and confidence intervals: ordinary least squares ("ols") or mixed-effects ("mixed")

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

sep_reps

Whether to calculate summary statistics on the groups with replicates combined. The current default FALSE combines replicates, but future releases will default to TRUE providing replicate-specific summaries.

ci_method

The method used to compute confidence intervals for the mixed-effects model: "Wald", "profile", or "boot" passed to lme4::confint.merMod().

Value

a ggplot

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.

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, sep_reps = FALSE)


atp_plot(energetics, basal_vs_max = "max", sep_reps = FALSE)


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

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


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