plot_samples: Informative plots to investigate samples

In ahmohamed/lipidr: Data Mining and Analysis of Lipidomics Datasets

Informative plots to investigate samples

Description

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.

Usage

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)
plot_samples(
  data_normalized[, data_normalized$group == "QC"],
  type = "boxplot",
  measure = "Retention Time", log = FALSE
)

ahmohamed/lipidr documentation built on July 7, 2023, 2:22 a.m.