Description Usage Arguments Value Examples
the cellAggregator function
1 2 3 |
numCells |
vector of the number of cells per cell population |
numProtsPerCell |
matrix (number of cell populations x number of protein types) specifying number of proteins per cell |
bindingAffinity |
matrix of binding affinities between proteins (should be symmetric matrix) |
timesteps |
(default 100) number of timesteps |
burnIn |
(default 0.75) consider the last burnIn proportion of timesteps for index calculation |
verbose |
(default TRUE) print messages |
includeListOfGraphs |
(default TRUE) include list of graphs in results object |
plot |
(default FALSE) if TRUE prints a breakdown of the input parameters |
... |
arguments go to bindProteins() |
cellGraph |
is an igraph object specifying the cell-cell bindings (only one of proteinGraph or cellGraph should be specified) |
list
cellAggregationResult object containing the input parameters: numCells, numProtsPerCell, bindingAffinity, timesteps, burnIn, verbose, includeListOfGraphs; and output objects: listofCellGraphs (list of cell graphs per timestep), listofProteinGraphs (list of protein graphs per timestep), listoftIndex (list of t index per timestep), listofTabulation (list of tabulation of proteins per timestep), and t_index (final t index summary value across entire simulation).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | numCells = c(25,25)
numProtsPerCell = rbind(c(5,0,0),c(5,5,5))
bindingAffinity = cbind(c(1,0,0), c(0,1,0), c(0,0,1))
cellAggregationResult = cellAggregator(
numCells,
numProtsPerCell,
bindingAffinity,
timesteps = 100,
burnIn = 0.75,
verbose = TRUE,
includeListOfGraphs = TRUE,
plot = TRUE
)
cellAggregationResult$t_index
unlist(cellAggregationResult$listoftIndex)
cellAggregationBarplot(cellAggregationResult)
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