plot: Plots an optimized cellular hierarchy
In RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry

Description Usage Arguments Author(s) See Also

Plots an optimized cellular hierarchy

## S4 method for signature 'OptimizedHierarchy,ANY'
plot(x, phenotypeScores, phenotypeCodes, marker.names,
                 partitions.per.marker = NULL, 
uniformColors = FALSE, ylab = NULL, xlab = NULL, colors = c("blue",
"cyan", "yellow", "red"), edgeWeights = TRUE, edgeLabels = TRUE,
nodeLabels = TRUE, min.score = NA, max.score = NA, cell.proportions =
NULL, min.proportion = NA, max.proportion = NA, proportion.colors =
c("black", "white"), node.lwd = 5, root.name = "All Cells",
legend.size=1.25, plot.legend=TRUE, textcol=par('fg'))

`x`	An OptimizedHierarchy object as generated by RchyOptimyx.
`phenotypeScores`	The score vector used for determining the colors of the nodes.
`phenotypeCodes`	A vector of strings of length N (the number of markers) for each phenotype measured. For every phenotype, the character corresponding to a given marker can be 0, 1, 2, etc for neutral, negative, positive, bright, etc. See the provided vigenette for more details and examples.
`marker.names`	A vector of characters representing the names of all markers involved in the analysis.
`partitions.per.marker`	A vector of integers, one per marker, describing the number of partitions per marker. Default is 2 (positive and negative) for all markers.
`uniformColors`	Boolean variable. If TRUE, the graph will not have any colors.
`ylab`	y-axis label of the density plot on the right.
`xlab`	x-axis label of the density plot of the phenotype cell proportion in the buttom.
`colors`	Color vector indicating colors to be used in the right pallet.
`edgeWeights`	Boolean value indicating weather edgeWeights should be plotted or not.
`edgeLabels`	Boolean value indicating weather edgeLabels should be plotted or not.
`nodeLabels`	Boolean value indicating weather nodeLabels should be plotted or not.
`min.score`	Double value indicating the minimum value of scores. Default value will use minimum node scores of the given `OptimizedHierarchy` object.
`max.score`	Double value indicating the maximum value of scores. Default value will use maximum node scores of the given `OptimizedHierarchy` object.
`cell.proportions`	The score vector used to determine the color of node borders to illustrate phenotype cell proportions.
`min.proportion`	Double value indicating the minimum value of the cell proportions. Default value will use minimum cell proportion of the given `OptimizedHierarchy` object.
`max.proportion`	Double value indicating the minimum value of the cell proportions. Default value will use minimum cell proportion of the given `OptimizedHierarchy` object.
`proportion.colors`	Color vector indicating colors to be used in the buttom pallet.
`node.lwd`	Integer value indicating node border width.
`root.name`	Character value indicating the root node's name.
`legend.size`	Size of the color legend in inches.
`plot.legend`	Boolean indicating wether the color legend should be plotted.
`textcol`	The color of the axis label(s) for the color legend(s).