move2Ds: Displays a spatial proteomics animation

Description Usage Arguments Value Author(s) See Also Examples

View source: R/plotting2.R

Description

Given two MSnSet instances of one MSnSetList with at least two items, this function produces an animation that shows the transition from the first data to the second.

Usage

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move2Ds(object, pcol, fcol = "markers", n = 25, hl)

Arguments

object

An linkS4class{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.

n

Number of frames, Default is 25.

hl

An optional instance of class linkS4class{FeaturesOfInterest} to track features of interest.

Value

Used for its side effect of producing a short animation.

Author(s)

Laurent Gatto

See Also

plot2Ds to a single figure with the two datasets.

Examples

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library("pRolocdata")
data(dunkley2006)

## Create a relevant MSnSetList using the dunkley2006 data
xx <- split(dunkley2006, "replicate")
xx1 <- xx[[1]]
xx2 <- xx[[2]]
fData(xx1)$markers[374] <- "Golgi"
fData(xx2)$markers[412] <- "unknown"
xx@x[[1]] <- xx1
xx@x[[2]] <- xx2

## The features we want to track
foi <- FeaturesOfInterest(description = "test",
                          fnames = featureNames(xx[[1]])[c(374, 412)])

## (1) visualise each experiment separately
par(mfrow = c(2, 1))
plot2D(xx[[1]], main = "condition A")
highlightOnPlot(xx[[1]], foi)
plot2D(xx[[2]], mirrorY = TRUE, main = "condition B")
highlightOnPlot(xx[[2]], foi, args = list(mirrorY = TRUE))

## (2) plot both data on the same plot
par(mfrow = c(1, 1))
tmp <- plot2Ds(xx) 
highlightOnPlot(data1(tmp), foi, lwd = 2)
highlightOnPlot(data2(tmp), foi, pch = 5, lwd = 2)

## (3) create an animation
move2Ds(xx, pcol = "replicate")
move2Ds(xx, pcol = "replicate", hl = foi)

pRoloc documentation built on Nov. 8, 2020, 6:26 p.m.