Informative plots to investigate samples — plot

lipidr supports two types of plots for sample quality checking.

tic plots a bar chart for total sample intensity.

boxplot plots a boxplot chart to examine the distribution of values per sample.

plot_samples(
  data,
  type = c("tic", "boxplot"),
  measure = "Area",
  log = TRUE,
  color = NULL
)

Arguments

data: LipidomicsExperiment object.
type: plot type, either tic or boxplot. Default is tic.
measure: Which measure to use as intensity, usually Area, Area Normalized or Height. Default is Area
log: Whether values should be log2 transformed. Default is TRUE
color: The column name of a sample annotation to be used as color

Value

A ggplot object.

Examples

data(data_normalized)

plot_samples(data_normalized, type = "tic", "Area", log = TRUE)

plot_samples(data_normalized, type = "tic", "Background", log = FALSE)
#> Warning: Removed 1 rows containing non-finite values (`stat_summary()`).

plot_samples(
  data_normalized[, data_normalized$group == "QC"],
  type = "boxplot",
  measure = "Retention Time", log = FALSE
)
#> Warning: Removed 1 rows containing non-finite values (`stat_boxplot()`).