SOMMD (version 0.1.2)

trace.path: Trace pathway

Description

Function trace pathway sampled on the SOM

Usage

trace.path(
  SOM,
  start = 1,
  end = length(SOM$unit.classif),
  N = 1,
  draw.stride = 1,
  pts.scale = 1,
  lwd.scale = 1
)

Value

Called for its effect.

Arguments

SOM

the SOM object

start

a vector containing the start frames of each replica (usually contained in trj$start if replicas were merged with cat_trj)

end

a vector containing the end frames of each replica (usually contained in trj$end if replicas were merged with cat_trj)

N

The portion of simulation that one want to plot

draw.stride

used to plot the pathways with a stride (useful for very complex pathways)

pts.scale

a number to scale up or down the size of the circles

lwd.scale

a number to scale up or down the size of the lines

Author

Stefano Motta

Examples

# Read the trajectory
trj <- read.trj(trjfile = system.file("extdata", "HIF2a-MD.xtc", package = "SOMMD"),
  topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))
#Read example SOM data
som_model <- readRDS(system.file("extdata", "SOM_HIFa.rds", package = "SOMMD"))
#trace pathway sampled on the SOM
trace.path(som_model, start=trj$start, end=trj$end, N=1, pts.scale=0.5)