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Rate plot

Source: R/rate_plot.R
rate_plot.Rd

Generate OCR and ECAR plots

Usage

rate_plot(
  seahorse_rates,
  measure = "OCR",
  assay = "MITO",
  model = "ols",
  error_bar = "ci",
  conf_int = 0.95,
  group_label = "Experimental group",
  linewidth = 2,
  sep_reps = FALSE,
  ci_method = "Wald"
)

Arguments

seahorse_rates

data.table Seahorse OCR and ECAR rates (imported using read_data function)

measure

Whether to plot "OCR" or "ECAR"

assay

What assay to plot (e.g. "MITO" or "GLYCO")

model

The model used to estimate mean and confidence intervals:

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

group_label

Label for the experimental group to populate the legend title

linewidth

Width for the lines, passed to geom_line()

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

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
seahorse_rates <- read_data(rep_list, sheet = 2)
rate_plot(
  seahorse_rates,
  measure = "OCR",
  error_bar = "ci",
  conf_int = 0.95,
  sep_reps = FALSE
)

rate_plot(
  seahorse_rates,
  measure = "OCR",
  error_bar = "ci",
  conf_int = 0.95,
  sep_reps = TRUE
)