plot: Plots an optimized cellular hierarchy

Description Usage Arguments Author(s) See Also

Description

Plots an optimized cellular hierarchy

Usage

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## 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'))

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).

Author(s)

Nima Aghaeepour <[email protected]> and Adrin Jalali <[email protected]>

See Also

RchyOptimyx-methods


RchyOptimyx documentation built on May 6, 2019, 2:15 a.m.