plot {RchyOptimyx} | R Documentation

## Plots an optimized cellular hierarchy

### Description

Plots an optimized cellular hierarchy

### Usage

    ## 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 <naghaeep@stanford.edu> and Adrin Jalali <ajalali@bccrc.ca>

### See Also

`RchyOptimyx-methods`

[Package RchyOptimyx version 2.20.0 Index]