get_alluvialplot: Plot alluvial plot of dynamic community membership
In jevansbio/MajorTrackR: MajorTrackR

Description Usage Arguments Details Examples

View source: R/MTRfuncs.R

Plots dynamic communities and the movements between them as an alluvial plot https://en.wikipedia.org/wiki/Alluvial_diagram

get_alluvialplot(
  track,
  allcols = NULL,
  fluxbysource = T,
  fluxsinglecol = T,
  fluxmovecol = "grey",
  fluxsinglecolremain = T,
  fluxremaincol = "grey",
  fluxalpha = 0.4,
  figwidth = 8,
  figheight = 2,
  rlabels = NULL,
  rstart = NULL,
  rstop = NULL,
  rmargins = c(0, 0.2, 1, 1),
  cwidth = 0.2,
  clusterlw = 0.5,
  labelsize = -1,
  reimport = T,
  removefile = T,
  exportfilename = "Rplot.png"
)

`track`	A MajorTrack object as produced by `do_track`.
`allcols`	A vector of colours, the same length at the number of unique dynamic communities in the MajorTrack object. Defaults to rainbow colours.
`fluxbysource`	Boolean. If TRUE, the connecting fluxes between timesteps will be coloured the same as the dynamic community from which they originate. Defaults to TRUE.
`fluxsinglecol`	Boolean. If TRUE, the connecting fluxes between timesteps will be a single colour as defined by `fluxmovecol`. Overrides fluxbysource.
`fluxmovecol`	Single colour of movements between different dynamic communities in different timesteps. Defaults to "grey".
`fluxsinglecolremain`	Boolean. If TRUE fluxes between the same dynamic community in different timesteps will be a single colour as defined by `fluxremaincol`. Defaults to TRUE.
`fluxremaincol`	Single colour for remaining in the same dynamic community in different timesteps. Defaults to "grey".
`fluxalpha`	Transparency of fluxes, where 1 is opaque and 0 is invisible. Defaults to 0.4
`figwidth`	Width of figure in inches. Defaults to 8.
`figheight`	height of figure in inches. Defaults to 2.
`rlabels`	Vector of labels that, if supplied, will override the timestep labels.
`rstart`	Integer specifying timestep at which to start plotting.
`rstop`	Integer specifying timestep at which to stop plotting.
`rmargins`	Vector of numbers between 0 and 1 in the format `c(left,bottom,right,top)`. Specifies a rectangle in which the alluvial plot (blocks and fluxes) is placed in the overall plotting area. By default the alluvial plot takes up the entirety of the plotting area, except for the bottom where a gap is left for the labels: `c(0,0.2,1,1)`.
`cwidth`	Number between 0 and 1 defining cluster width. 0 will hide clusters, 1 will leave no room between clusters. Defaults to 0.2
`clusterlw`	Number between 0 and 1 defining line width of cluster borders. Defaults to 0.5. Currently has no effect.
`labelsize`	Number defining size of per cluster labels. Defaults to 0, hiding labels.
`reimport`	Boolean. If TRUE, the python figure will be imported into R. Defaults to TRUE.
`removefile`	Boolean. If TRUE, the exported python figure will be deleted when the function is finished. Defaults to TRUE.
`exportfilename`	String giving the name and path of the exported file. Defaults to "Rplot.png"

The R function for the MT alluvial plots is a wrapper for the python plotting functions.

If reimport is TRUE it will run the plotting code, export an image then bring it back into R. By default the image file will then be removed.

The code attempts to place the R margins and axis in the same positions as those in the python plot. There is a chance this might fail on some graphics devices. If succesful the resulting plotting device will have an x-axis where each tick is a timestep.

Combining fluxbysource, fluxsinglecol and fluxsinglecolremain will produce different effects. fluxsinglecol being TRUE will colour all fluxes the same. If fluxsinglecolremain is also TRUE, this will result in remain fluxes being one colour and all other fluxes (moves, splits, merges) being another colour. If fluxsinglecol is FALSE and fluxbysource is TRUE then fluxes will be coloured by the community they originate from. and all other fluxes (moves, splits, merges) being another colour. If fluxsinglecol is FALSE and fluxbysource is also FALSE then fluxes will be coloured by the community they are heading toward. Both these combinations can further be combined with fluxsinglecolremain being TRUE to separate remain fluxes and all other fluxes.

data(allnets)
data(allnets)
#detect each networks communities
coms=lapply(allnets,function(x){
  igraph::cluster_louvain(x)
})
track = do_track(allnets, coms, history=1)
get_similarities(track)