hoeffDPlot {MatrixQCvis}R Documentation

Create a plot from a list of Hoeffding's D values

Description

The function 'hoeffDPlot' creates via 'ggplot' a violin plot per factor, a jitter plot of the data points and (optionally) connects the points via lines. 'hoeffDPlot' uses the 'plotly' package to make the figure interactive.

Usage

hoeffDPlot(df, lines = TRUE)

Arguments

df

'data.frame' containing one or multiple columns containing the Hoeffding's D statistics

lines

'logical', should points belonging to the same sample be connected

Details

The function 'hoeffDPlot' will create the violin plot and jitter plot according to the specified order given by the colnames of 'df'. 'hoeffDPlot' will thus internally refactor the 'colnames' of the supplied 'data.frame' according to the order of the 'colnames'.

Value

'gg' object from 'ggplot2'

Examples

## create se
set.seed(1)
a <- matrix(rnorm(10000), nrow = 1000, ncol = 10, 
            dimnames = list(1:1000, paste("sample", 1:10)))
a[c(1, 5, 8), 1:5] <- NA
cD <- data.frame(name = colnames(a), type = c(rep("1", 5), rep("2", 5)))
rD <- data.frame(spectra = rownames(a))
se <- SummarizedExperiment::SummarizedExperiment(assay = a, 
    rowData = rD, colData = cD)

tbl <- MAvalues(se, log2 = FALSE, group = "all")
hd_r <- hoeffDValues(tbl, "raw")

## normalized values
se_n <- se
assay(se_n) <- normalizeAssay(a, "sum")
tbl_n <- MAvalues(se_n, log2 = FALSE, group = "all")
hd_n <- hoeffDValues(tbl_n, "normalized")

df <- data.frame(raw = hd_r, normalized = hd_n)
hoeffDPlot(df, lines = TRUE)
hoeffDPlot(df, lines = FALSE)


[Package MatrixQCvis version 1.1.2 Index]