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.
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"))
