Plot protein boxplots — plot_protein

plot_protein_boxplot() plots boxplots for the specified proteins in the dataset. It annotates the boxplot with color for the selected case It is also possible to add points to the boxplot.

Usage

plot_protein_boxplot(
  join_data,
  variable = "Disease",
  proteins,
  case,
  points = TRUE,
  xaxis_names = FALSE,
  palette = NULL
)

Arguments

join_data: The dataset with the wide Olink data joined with the metadata.
variable: The variable that will be used as x and fill.
proteins: The proteins to include in the boxplot.
case: The case to annotate.
points: Whether to add points to the boxplot.
xaxis_names: Whether to show the x-axis names. Default is FALSE.
palette: The color palette to use. Default is "red3" for the annotated case

Value

The boxplot panel with the selected proteins.

Examples

# Prepare the data
wide_data <- widen_data(example_data)
join_data <- wide_data |>
  dplyr::left_join(example_metadata |> dplyr::select(DAid, Disease, Sex))
#> Joining with `by = join_by(DAid)`

# Boxplots for AARSD1 and ABL1 in AML
plot_protein_boxplot(join_data,
                     proteins = c("AARSD1", "ABL1"),
                     case = "AML",
                     palette = "cancers12")
#> Warning: Removed 68 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 8 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).
#> Warning: Removed 60 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_point()`).