plot_normalization {DEP} | R Documentation

## Visualize normalization

### Description

`plot_normalization` generates boxplots of all conditions for input objects, e.g. before and after normalization.

### Usage

    plot_normalization(se, ...)

### Arguments

`se` | SummarizedExperiment, Data object, e.g. before normalization (output from `make_se()` or `make_se_parse()`).
`...` | Additional SummarizedExperiment object(s), E.g. data object after normalization (output from `normalize_vsn`).

### Value

Boxplots of all conditions for input objects, e.g. before and after normalization (generated by `ggplot`). Adding components and other plot adjustments can be easily done using the ggplot2 syntax (i.e. using '+')

### Examples

    # Load example
    data <- UbiLength
    data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
    data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

    # Make SummarizedExperiment
    columns <- grep("LFQ.", colnames(data_unique))
    exp_design <- UbiLength_ExpDesign
    se <- make_se(data_unique, columns, exp_design)

    # Filter and normalize
    filt <- filter_missval(se, thr = 0)
    norm <- normalize_vsn(filt)

    # Plot normalization
    plot_normalization(se, filt, norm)

[Package DEP version 1.6.1 Index]