draw.bn: Draws a Bayesian network

In Pigengene: Infers biological signatures from gene expression data

Description

Draws the BN using appropriate colors and font size.

Usage

draw.bn(BN, plotFile = NULL, inputType = "ENTREZIDat", edgeColor = "blue",
  DiseaseCol = "darkgreen", DiseaseFill = "red", DiseaseChildFill = "pink",
  nodeCol = "darkgreen", nodeFill = "yellow", moduleNamesFile = NULL,
  mainText = NULL, nodeFontSize = 14 * 1.1, verbose = 0)

Arguments

BN	An object of bn-class
plotFile	If not NULL, the plot will be saved here.
inputType	The type of gene IDs in BN
edgeColor	The color of edges
DiseaseCol	The color of the border of the Disease node
DiseaseFill	The color of the area inside the Disease node
DiseaseChildFill	The color of the area inside the children of the Disease node
nodeCol	The color of the border of the usual nodes excluding Disease and its children
nodeFill	The color of the area inside the usual nodes
moduleNamesFile	An optional csv file including the information to rename the nodes name. See coderename.node.
mainText	The main text shown at the top of the plot
nodeFontSize	Adjusts the size of nodes
verbose	The integer level of verbosity. 0 means silent and higher values produce more details of computation.

Value

A list with following components:

call	The call that created the results
BN	An echo of input BN argument
renamedBN	An object of bn-class when moduleNamesFile is provided
gr	The full output of graphviz.plot function

Author(s)

Habil Zare

See Also

bnlearn-package, Pigengene-package, learn.bn, graph-class

Examples

## See lear.bn function.

Example output

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Pigengene documentation built on Nov. 8, 2020, 6:47 p.m.