plot2Ds: Draw 2 data sets on one PCA plot
In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description Usage Arguments Value Author(s) See Also Examples

Takes 2 linkS4class{MSnSet} instances as input to plot the two data sets on the same PCA plot. The second data points are projected on the PC1 and PC2 dimensions calculated for the first data set.

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plot2Ds(object, pcol, fcol = "markers", cex.x = 1, cex.y = 1,
  pch.x = 21, pch.y = 23, col, mirrorX = FALSE, mirrorY = FALSE,
  plot = TRUE, ...)

`object`	An `MSnSet` or a `MSnSetList`. In the latter case, only the two first elements of the list will be used for plotting and the others will be silently ignored.
`pcol`	If `object` is an `MSnSet`, a `factor` or the name of a phenotype variable (`phenoData` slot) defining how to split the single `MSnSet` into two or more data sets. Ignored if `object` is a `MSnSetList`.
`fcol`	Feature meta-data label (fData column name) defining the groups to be differentiated using different colours. Default is `markers`. Use `NULL` to suppress any colouring.
`cex.x`	Character expansion for the first data set. Default is 1.
`cex.y`	Character expansion for the second data set. Default is 1.
`pch.x`	Plotting character for the first data set. Default is 21.
`pch.y`	Plotting character for the second data set. Default is 23.
`col`	A vector of colours to highlight the different classes defined by `fcol`. If missing (default), default colours are used (see `getStockcol`).
`mirrorX`	A `logical` indicating whether the x axis should be mirrored?
`mirrorY`	A `logical` indicating whether the y axis should be mirrored?
`plot`	If `TRUE` (default), a plot is produced.
`...`	Additinal parameters passed to `plot` and `points`.

Used for its side effects of producing a plot. Invisibly returns an object of class plot2Ds, which is a list with the PCA analyses results (see prcomp) of the first data set and the new coordinates of the second data sets, as used to produce the plot and the respective point colours. Each of these elements can be accessed with data1, data2, col1 and code2 respectively.

Laurent Gatto

See plot2D to plot a single data set and move2Ds for a animation.

library("pRolocdata")
data(tan2009r1)
data(tan2009r2)
msnl <- MSnSetList(list(tan2009r1, tan2009r2))
plot2Ds(msnl)
## tweaking the parameters
plot2Ds(list(tan2009r1, tan2009r2),
        fcol = NULL, cex.x = 1.5)
## input is 1 MSnSet containing 2 data sets
data(dunkley2006)
plot2Ds(dunkley2006, pcol = "replicate")
## no plot, just the data
res <- plot2Ds(dunkley2006, pcol = "replicate",
               plot = FALSE)
res
head(data1(res))
head(col1(res))