plot2Ds: Draw 2 data sets on one PCA plot

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Draw 2 data sets on one PCA plot

Description

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.

Usage

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

Arguments

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.

Value

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.

Author(s)

Laurent Gatto

See Also

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

Examples

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))

lgatto/pRoloc documentation built on Oct. 23, 2024, 12:51 a.m.