In wmoldham/seahorse: Analyze Seahorse Bioenergetic Data

#| label = setup, 
#| include = FALSE

knitr::opts_chunk$set(echo = FALSE)

library(seahorse)
ggplot2::theme_set(ggplot2::theme_bw())

Experiment Description

:::: {.columns}

::: {.column width="50%"}

#| label = wells

params$wells |> 
  dplyr::group_by(group) |>
  gt::gt(row_group_as_column = TRUE) |> 
  gt::tab_header(title = "Samples") |>
  gt::tab_stubhead(label = "group") |>
  gt::sub_missing()

:::

::: {.column width="50%"}

#| label = stages

params$stages |> 
  dplyr::group_by(stage) |> 
  gt::gt(row_group_as_column = TRUE) |> 
  gt::tab_header(title = "Design") |> 
  gt::tab_stubhead(label = "stage") |> 
  gt::sub_missing()

:::

::::

#| label = seahorse

cells_list <- purrr::map(params$cells, format_cells)

sea <- 
  purrr::map2(
    params$data, 
    cells_list, 
    \(x, y) Seahorse(
      path = x, 
      wells = wells, 
      stages = stages, 
      cells = y, 
      units = params$units, 
      bf = params$bf, 
      cf = params$cf
    )
  )

#| label = headers

has_cells <- !is.na(params$cells)

#| label = header_normalization,
#| eval = has_cells, 
#| results = "asis"

cat("## Normalization")

#| label = normalization-plot,
#| eval = has_cells, 
#| results = "hide",
#| fig.align = "center"

purrr::map(
  sea, 
  \(x) plot(x, "cells") + ggplot2::ggtitle(filename(x))
)