Coverage heatmap — plot_coverage

Coverage heatmap with color indicating specific value

Usage

plot_coverage_heatmap(
  x_dat,
  protein = x_dat[["Protein"]][1],
  state = NULL,
  value = NULL,
  time_t = NULL,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

x_dat: data created using calculate_ or create_ function
protein: selected protein
state: selected biological state
value: value to be presented
time_t: chosen time point
interactive: logical, whether plot should have an interactive layer created with with ggiraph, which would add tooltips to the plot in an interactive display (HTML/Markdown documents or shiny app)

Value

a ggplot object

Details

Plots standard protein coverage but colored with desired value.

Examples

uptake_dat <- create_uptake_dataset(alpha_dat, states = "Alpha_KSCN")
plot_coverage_heatmap(uptake_dat)

plot_coverage_heatmap(x_dat = uptake_dat, value = "frac_deut_uptake", time_t = 0.167)
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the HaDeX package.
#>   Please report the issue to the authors.
#> Ignoring unknown labels:
#> • colour : "Exposure"

plot_coverage_heatmap(uptake_dat, value = "err_frac_deut_uptake", time_t = 0.167)
#> Ignoring unknown labels:
#> • colour : "Exposure"


diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_coverage_heatmap(diff_uptake_dat)

plot_coverage_heatmap(diff_uptake_dat, value = "diff_frac_deut_uptake")
#> No time point selected!

plot_coverage_heatmap(diff_uptake_dat, value = "diff_frac_deut_uptake", time_t = 0.167)
#> Ignoring unknown labels:
#> • colour : "Exposure"

plot_coverage_heatmap(diff_uptake_dat, value = "err_diff_frac_deut_uptake", time_t = 0.167)
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
#> Ignoring unknown labels:
#> • colour : "Exposure"


auc_dat <- calculate_auc(create_uptake_dataset(alpha_dat))
plot_coverage_heatmap(auc_dat, value = "auc")
#> Ignoring unknown labels:
#> • colour : "Exposure"


bex_dat <- calculate_back_exchange(alpha_dat, state = "Alpha_KSCN")
plot_coverage_heatmap(bex_dat, value = "back_exchange")
#> Ignoring unknown labels:
#> • colour : "Exposure"