distSample {MatrixQCvis} | R Documentation

## Create a heatmap using distance information between samples

### Description

The function 'distSample' creates a heatmap from a distance matrix created by the function 'distShiny'. The heatmap is annotated by the column specified by the 'label' column in 'colData(se)'.

### Usage

    distSample(d, se, label = "name", title = "raw", ...)

### Arguments

`d` | 'matrix' containing distances, obtained from 'distShiny'
`se` | 'SummarizedExperiment'
`label` | 'character', refers to a column in 'colData(se)'
`title` | 'character'
`...` | further arguments passed to 'ComplexHeatmap::Heatmap'

### Details

Internal use in 'shinyQC'

### Value

'plotly'

### Examples

    ## create se
    a <- matrix(1:100, nrow = 10, ncol = 10,
                dimnames = list(1:10, paste("sample", 1:10)))
    a[c(1, 5, 8), 1:5] <- NA
    set.seed(1)
    a <- a + rnorm(100)
    a_i <- imputeAssay(a, method = "MinDet")
    cD <- data.frame(name = colnames(a_i),
        type = c(rep("1", 5), rep("2", 5)))
    rD <- data.frame(spectra = rownames(a_i))
    se <- SummarizedExperiment::SummarizedExperiment(assay = a_i, rowData = rD,
        colData = cD)

    dist <- distShiny(a_i)
    distSample(dist, se, label = "type", title = "imputed",
        show_row_names = TRUE)

[Package MatrixQCvis version 1.2.4 Index]