plot {RchyOptimyx} | R Documentation |
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 |
max.score |
Double value indicating the maximum value of scores. Default value will use maximum node scores of the given |
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 |
max.proportion |
Double value indicating the minimum value of the cell proportions. Default value will use minimum cell proportion of the given |
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). |
Nima Aghaeepour <naghaeep@stanford.edu> and Adrin Jalali <ajalali@bccrc.ca>