RnaSeqTutorial-heatscatter: Heatscatter based plot
In UPSCb/RnaSeqTutorial: RNA-Seq Tutorial

Description Usage Arguments Details See Also Examples

A based on the LSD package heatscatter function. It is an adaptation of the MA plot from the DESeq package plotMA function.

plotMALSD(x, ylim, sign = 0.05, col = "forestgreen",
  linecol = "#00000080", xlab = "mean of normalized counts",
  ylab = expression(log[2] ~ fold ~ change), log = "x", cex = 0.45,
  ...)

`x`	a data.frame object, the result of the `DESeq` analysis. It must contain the following columns: `baseMean`, `log2FoldChange` and `padj`.
`ylim`	the y axis limits
`sign`	the significance threshold cutoff (on the adjusted p-values). Default to 5 percent
`col`	the color to mark the points exceeding the significant threshold. Default to 'forestgreen'
`linecol`	the line color, default to"#00000080"
`xlab`	the x axis label. Default to "mean of normalized counts".
`ylab`	the y axis lable. Default to "dispersion" or "expression(log[2] ~ fold ~ change)" for the dispertion and MA plot, respectively.
`log`	whether to report the axis on a log scale. default to "x" and "xy" for the MA and dispersion plot, respectively. See `par` for more details.
`cex`	the character extension, default to 0.45
`...`	additional argument passed to the `heatscatter` function.

The plot is a modification that integrate a third dimension as a colouring shade from blue (sparse) to yellow (dense). Grey represent outlier data points. This is based on the heatscatter function of the LSD package.

LSD, heatscatter, plotDispEsts, plotMA

## Not run: 
## TODO add an object after putting results in the data folder
## and use that for plotting the example

data(RST-DataFrame)
plotMALSD(dataFrame)

## End(Not run)