plotTranslocations | R Documentation |
Produces a chord diagram (circos plot) or an alluvial plot (also known as a Sankey diagram) to show changes in location between two conditions or datasets.
plotTranslocations( params, type = "alluvial", all = FALSE, fcol, col, labels = TRUE, labels.par = "adj", cex = 1, spacer = 4, ... )
params |
An instance of class |
type |
A |
all |
A logical specifying whether to count all proteins or only show
those that have changed in location between conditions. Default is
|
fcol |
If |
col |
A list of colours to define the classes in the data. If not
defined then the default |
labels |
Logical indicating whether to display class/organelle labels
for the chord segments or alluvial stratum. Default is |
labels.par |
If |
cex |
Text size. Default is 1. |
spacer |
A |
... |
Additional arguments passed to the |
Returns a directional circos/chord diagram showing the translocation
of proteins between conditions. If type = "alluvial"
ouput is a
ggplot
object.
## Generate some example data library("pRolocdata") data("tan2009r1") set.seed(1) tansim <- sim_dynamic(object = tan2009r1, numRep = 4L, numDyn = 100L) data <- tansim$lopitrep control <- data[1:2] treatment <- data[3:4] ## fit GP params gpParams <- lapply(tansim$lopitrep, function(x) fitGPmaternPC(x, hyppar = matrix(c(0.5, 1, 100), nrow = 1))) ## run bandle res <- bandle(objectCond1 = control, objectCond2 = treatment, gpParams = gpParams, fcol = "markers", numIter = 5L, burnin = 1L, thin = 2L, numChains = 1, BPPARAM = SerialParam(RNGseed = 1), seed = 1) ## Process the results bandleres <- bandleProcess(res) ## plot the results plotTranslocations(bandleres) plotTranslocations(bandleres, type = "chord")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.