hoeffDPlot {MatrixQCvis} | R Documentation |
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.
hoeffDPlot(df, lines = TRUE)
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 |
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'.
'gg' object from 'ggplot2'
## 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)