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
plot_samples( data, type = c("tic", "boxplot"), measure = "Area", log = TRUE, color = NULL )
plot type, either
Which measure to use as intensity, usually Area,
Area Normalized or Height. Default is
Whether values should be log2 transformed. Default is
The column name of a sample annotation to be used as color
A ggplot object.
data(data_normalized) plot_samples(data_normalized, type = "tic", "Area", log = TRUE)#> Warning: `fun.y` is deprecated. Use `fun` instead.plot_samples(data_normalized, type = "tic", "Background", log = FALSE)#> Warning: `fun.y` is deprecated. Use `fun` instead.#> 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).