general.scatter_by: Function to create scatterplots, color-coded by subgroups
In jhooge/BioViz: BiomarkerVizard

Description Usage Arguments Value Author(s) Examples

Function to create scatterplots, color-coded by subgroups

general.scatter_by(x, y, by = NULL, col.by = 1:length(unique(by)),
  name.by = "", mar = c(6, 4, 2, 1), xlab = "", ylab = "",
  xlim = NULL, ylim = NULL, mark = NULL, xlog = FALSE, ylog = FALSE,
  pch = 1, cex.pch = 0.75, add.reg = FALSE, add.mean = FALSE,
  add.leg = TRUE, cex.mean = 1, file.name = NULL, png.out = TRUE,
  png.width = 6, png.height = 5, ...)

`x`	numeric vector (Required)
`y`	second numeric vector of the same length than 'x' (Required)
`by`	character or factor vector of the same length than 'x' to specify by-groups used for color-coding (Default: Null)
`col.by`	colors for the 'by'-groups(Default: 1:length(unique(by)))
`name.by`	character, name of the 'by'-variable, used as legend-title
`mar`	margins of the plot as in 'par()' (Default: c(6,4,1,1))
`xlab`	character, labels for the x-axis (Default: ”)
`ylab`	character, labels for the y-axis (Default: ”)
`xlim`	Range of the x-axis (Default: Null)
`ylim`	Range of the y-axis (Default: Null)
`mark`	TODO: This parameter was not documented in original code (Default: Null)
`xlog`	TRUE/FALSE is x log-transformed? if yes, axis annotation will account for that (Default: FALSE)
`ylog`	TRUE/FALSE is y log-transformed? if yes, axis annotation will account for that (Default: FALSE)
`pch`	symbol for the jitter points (default=1, i.e. the same symbol for all points), if at least as many symbols as the number of levels of the 'by.col' variable are given, symbol coding is used in addition to color coding. (Default: 1)
`cex.pch`	size of the points (Default: 0.75)
`add.reg`	TRUE/FALSE if true, adds a regression line (Default: FALSE)
`add.mean`	TODO: This parameter was not documented in original code (Default: FALSE)
`add.leg`	TRUE/FALSE if true and 'by' is specified, a legend is added to the plot (Default: TRUE)
`cex.mean`	TODO: This parameter was not documented in original code (Default: 1)
`file.name`	name for the PNG output file (without '.png' ending) (Default: NULL)
`png.out`	TRUE/FALSE if true, a png file is created as output, otherwise the plot is created in the R graphic device (Default: TRUE)
`png.width`	width of PNG file in inches (Default: 6)
`png.height`	height of PNG file in inches (Default: 5)
`...`	Additional parameters for par()

PNG files with the scatterplot ('file.name.png') numeric vector with size of the PNG-file in inches for rescaling in RTF

Sebastian Voss, Adam Skubala

## Not run: 
set.seed(42)
x <- rnorm(500)
y <- x^2+rnorm(500)
by <- factor(c(rep('male', 250),
               rep('female',250)),
             levels=c('male','female'))

general.scatter_by(x, y, by=by, col.by=c('skyblue','tomato'), name.by="Sex",
                   xlab="Sex", ylab="Biomarker", file.name="test", add.reg=TRUE,
                   mar=c(7,4,4,2), xlim=range(x), ylim=range(y), 
                   pch <- c(1, 4), xlog=TRUE, add.mean=TRUE)

## End(Not run)