graphDispParams: Class '"graphDispParams"'

In dbottomly/HitWalker: Network-based variant prioriziation using functional assay scores

Description

A parameter class controlling aspects of plot creation and display.

Objects from the Class

Objects can be created by calls of the form makeGraphDispParams(shape.mapping.func, style.mapping.func, file.name, width, height,label.sep, max.plot.vars, max.plot.hits, plot.func, label.func.list, name.text.sep, node.comb.func, hit.colors,query.color, collapse.char, default.color, default.border). Or equivalently through new("graphDispParams", ...)

Slots

shape.mapping.func:

Object of class "function" Maps a data.frame split by the summary ID to a node shape.

style.mapping.func:

Object of class "function" Maps a data.frame split by the summary ID to a style (i.e. line type).

file.name:

Object of class "character" A vector specifying the file name that the plot will be written to. Specify character(0) for on screen display.

width:

Object of class "numeric" Width of the plot in inches (if applicable)

height:

Object of class "numeric" Height of the plot in inches (if applicable)

hit.colors:

Object of class "character" A vector containing colors to be used for the nodes of the hit(s). The names should indicate the columns of the hit data.frame.

query.color:

Object of class "character" A vector of length 1 containing the color of the variant nodes.

default.color:

Object of class "character" A vector of length 1 containing the default node color.

collapse.char:

Object of class "character" A vector of length 1 containing the character delimiting multiple colors if a node falls into multiple color categories (e.g. has a variant and is a hit).

default.border:

Object of class "character" A vector of length 1 containing the default border color.

node.comb.func:

Object of class "function" A function that allows additional logic to be used in terms of combinations of node attributes when determining the final plot node attributes.

label.sep:

Object of class "character" A vector specifying the character used to break up labels onto different lines for each node.

max.plot.vars:

Object of class "numeric" The maximum number of variant nodes to consider for the visualization.

max.plot.hits:

Object of class "numeric" The maximum number of hit nodes to consider for the visualization.

plot.func:

Object of class "function" Function used for plotting (see HitWalker:::basic.plot.image).

label.func.list:

Object of class "list" A list that specifies the functions and ordering of the node labels.

name.text.sep:

Object of class "character" A vector specifying the character used to seperate the node name from the node labels.

Methods

Simple slot accession methods:

fileName

signature(obj = "graphDispParams")

fileName<-

signature(obj = "graphDispParams")

collapseChar

signature(obj = "graphDispParams")

collapseChar<-

signature(obj = "graphDispParams")

defaultBorder

signature(obj = "graphDispParams")

defaultBorder<-

signature(obj = "graphDispParams")

defaultColor

signature(obj = "graphDispParams")

defaultColor<-

signature(obj = "graphDispParams")

hitColors

signature(obj = "graphDispParams")

hitColors<-

signature(obj = "graphDispParams")

labelFuncList

signature(obj = "graphDispParams")

labelFuncList<-

signature(obj = "graphDispParams")

labelSep

signature(obj = "graphDispParams")

labelSep<-

signature(obj = "graphDispParams")

maxPlotHits

signature(obj = "graphDispParams")

maxPlotHits<-

signature(obj = "graphDispParams")

maxPlotVars

signature(obj = "graphDispParams")

maxPlotVars<-

signature(obj = "graphDispParams")

nameTextSep

signature(obj = "graphDispParams")

nameTextSep<-

signature(obj = "graphDispParams")

nodeCombinationFunc

signature(obj = "graphDispParams")

nodeCombinationFunc<-

signature(obj = "graphDispParams")

plotFunc

signature(obj = "graphDispParams")

plotFunc<-

signature(obj = "graphDispParams")

queryColor

signature(obj = "graphDispParams")

queryColor<-

signature(obj = "graphDispParams")

shapeFunc

signature(obj = "graphDispParams")

shapeFunc<-

signature(obj = "graphDispParams")

styleFunc

signature(obj = "graphDispParams")

styleFunc<-

signature(obj = "graphDispParams")

height

signature(obj = "graphDispParams")

height<-

signature(obj = "graphDispParams")

width

signature(obj = "graphDispParams")

width<-

signature(obj = "graphDispParams")

Author(s)

Daniel Bottomly

See Also

draw.graph.variantPriorResult, variantPriorResult

Examples

data(prior_obj, package="HitWalker")

graph.params <- makeGraphDispParams(file.name=character())
    
draw.graph.variantPriorResult(var.obj=prior.obj, graph.params)

dbottomly/HitWalker documentation built on May 15, 2019, 1:22 a.m.