Description Usage Arguments Details Value Author(s) See Also Examples
Plot methods for genotype-phenotype networks. plot.gnbp
and plot.dbn
can be used to plot networks in which evidence has been absorbed and propagated. The beliefs or Jeffrey's signed information for conditional gaussian and phenotypic states and Fold Changes for discrete bayesian networks is mapped onto the network. plot.gpfit
and plot.dbfit
are plot methods for objects of class "gpfit" and "dbnfit" respectively.
1 2 3 4 5 6 7 8 9 10 11 | ## S3 method for class 'gnbp'
plot(x, y="JSI",ncol = 1, col.palette,col.length = 100,
fontsize=14, fontcolor="black",...)
## S3 method for class 'dbn'
plot(x, y="state",ncol = 1, col.palette,col.length = 100,
fontsize=14, fontcolor="black",...)
## S3 method for class 'gpfit'
plot(x, fontsize=14, fontcolor="black",...)
## S3 method for class 'dbnfit'
plot(x, fontsize=14, fontcolor="black",...)
|
x |
An object of class "gnbp" ( |
y |
A character string. Valid options are |
ncol |
a positive integer specifying the column number of JSI / belief / FC to plot. By default, the first column will be used. |
col.palette |
A list of character strings. For For |
col.length |
a positive integer (default = 100) specifying the resolution of the colormap (number of colors) in case of |
fontsize |
a single numeric value. fontsize for node labels |
fontcolor |
fontcolor for node labels |
... |
further arguments to the function |
plot.gpfit
and plot.dbnfit
are generic plot methods for objects of class"gpfit" and "dbnfit" respectively that are output from the fit-methods. These are networks in which evidence has not been absorbed and propagated.
plot.gnbp
and plot.dbn
are generic plot methods for objects of class "gnbp" and "dbn" that are outputs from the absorb methods. These functions plot the genotype-phenotype networks in which evidence has been absorbed and propagated and maps the quantitative system wide effects on the network. Both conditional gaussian and discrete bayesian networks are supported. Users can specify the colormap options such as end colors for the positive and negative gradients and the resolution of the colormap. The default node shapes are "ellipse" for the phenotype nodes and "box" for genotype nodes.The d-separated nodes are white while the colored nodes are d-connected, with the color indicating the strength and direction of change. The node for which evidence is absorbed is colored green (default color).
x
is invisibly returned
Janhavi Moharil<janhavim@buffalo.edu>
absorb.gnbp
, absorb.dbn
, fit.gnbp
, fit.dbn
1 2 3 4 5 6 7 8 9 |
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