move2Ds {pRoloc} | R Documentation

## Displays a spatial proteomics animation

### 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

    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

    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)

[Package pRoloc version 1.28.0 Index]