plot_missval {DEP} | R Documentation

## Plot a heatmap of proteins with missing values

### Description

`plot_missval` generates a heatmap of proteins with missing values to discover whether values are missing by random or not.

### Usage

    plot_missval(se)

### Arguments

`se` | SummarizedExperiment, Data object with missing values.

### Value

A heatmap indicating whether values are missing (0) or not (1) (generated by `Heatmap`).

### 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, normalize and impute missing values
    filt <- filter_missval(se, thr = 0)

    # Plot missing values heatmap
    plot_missval(filt)

[Package DEP version 1.12.0 Index]