`lipidr`

supports two types of plots for to visualize at lipid classes.

`sd`

plots a bar chart for standard deviation of a certain measure in each
class. This plot type is usually used to look at standard deviations of
intensity in each class, but can also be used to look at different measures
such as `Retention Time`

, to ensure all lipids are eluted within the expected
range. To assess instrumental variation apply the function to technical
quality control samples.

`boxplot`

Plots a boxplot chart to examine the distribution of values per
class. This plot type is usually used to look at the intensity distribution
in each class, but can also be used to look at different measures, such as
`Retention Time`

or `Background`

.

plot_lipidclass(data, type = c("boxplot", "sd"), measure = "Area", log = TRUE)

data | LipidomicsExperiment object. |
---|---|

type | plot type, either |

measure | Which measure to plot the distribution of: usually Area,
Area Normalized, Height or Retention Time. Default is |

log | Whether values should be log2 transformed. Default is |

A ggplot object.

data(data_normalized) d_qc <- data_normalized[, data_normalized$group == "QC"] plot_lipidclass(d_qc, "sd", "Area", log = TRUE)#> Warning: `fun.y` is deprecated. Use `fun` instead.plot_lipidclass(d_qc, "sd", "Retention Time", log = FALSE)#> Warning: `fun.y` is deprecated. Use `fun` instead.#> Warning: Removed 1 rows containing non-finite values (stat_summary).plot_lipidclass(d_qc, "boxplot", "Area", log = TRUE)plot_lipidclass(d_qc, "boxplot", "Retention Time", log = FALSE)#> Warning: Removed 1 rows containing non-finite values (stat_boxplot).