Usage
"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'))
Arguments
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).