meanSdPlot {DEP} | R Documentation

## Plot row standard deviations versus row means

### Description

`meanSdPlot` generates a hexagonal heatmap of the row standard deviations versus row means from SummarizedExperiment objects. See `meanSdPlot`.

### Usage

    meanSdPlot(x, ranks = TRUE, xlab = ifelse(ranks, "rank(mean)", "mean"),
      ylab = "sd", pch, plot = TRUE, bins = 50, ...)

### Arguments

`x` | SummarizedExperiment, Data object.
`ranks` | Logical, Whether or not to plot the row means on the rank scale.
`xlab` | Character, x-axis label.
`ylab` | Character, y-axis label.
`pch` | Ignored - exists for backward compatibility.
`plot` | Logical, Whether or not to produce the plot.
`bins` | Numeric vector, Data object before normalization.
`...` | Other arguments, Passed to `stat_binhex`.

### Value

A scatter plot of row standard deviations versus row means(generated by `stat_binhex`)

### 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 meanSdPlot
    meanSdPlot(norm)

[Package DEP version 1.12.0 Index]