Browse code

Added information on the plotting function in RtreemixModel-class.Rd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@69937 bc3139a8-67e5-0310-9ffc-ced21a209358

Jasmina Bogojeska authored on 28/09/2012 10:41:29
Showing2 changed files

... ...
@@ -152,6 +152,9 @@ Class \code{"RtreemixData"}, directly.
152 152
       mixture model as a directed \code{graphNEL} object.}
153 153
     \item{numTrees}{\code{signature(object = "RtreemixModel")}: A method
154 154
     for obtaining the number of tree components building up the mixture model.}
155
+    \item{plot}{\code{signature(x = "RtreemixModel", y = "missing")}: A method for visualizing the tree components comprising a mutagenetic trees mixture model.  
156
+    The user can also specify the \code{fontSize} (the default value is 8) used for the text labels of the nodes and the edges of the plotted trees. Additionally, one can use the parameter \code{k} to plot a certain tree component from the 
157
+    mixture model.}
155 158
   }
156 159
 }
157 160
 \references{Learning multiple evolutionary pathways from cross-sectional
158 161
deleted file mode 100644
... ...
@@ -1,63 +0,0 @@
1
-\name{plot-methods}
2
-\docType{methods}
3
-
4
-\alias{plot}
5
-\alias{plot-methods}
6
-\alias{plot,RtreemixModel,missing-method}
7
-
8
-
9
-
10
-\title{Method for visualizing mutagenetic trees mixture models}
11
-\description{
12
-   Function for visualizing the tree components comprising a mutagenetic trees mixture model.  
13
-   The user can also specify the \code{fontSize} used for the text labels of the nodes and the edges of the plotted trees. 
14
-   Additionally, one can use the parameter \code{k} to plot a certain tree component from the 
15
-   mixture model. 
16
-}
17
-\details{
18
-    The value of \code{k} (that gives the tree component to be plotted) can take \code{"integer"} values from one to the number of tree components.  
19
-}
20
- 
21
-\usage{
22
-plot(x, y, \dots)
23
-}
24
-
25
-\arguments{
26
-  \item{x}{An \code{RtreemixModel} object giving the mixture model that should be visualized.}
27
-  \item{y}{Not specified.}
28
-  \item{\dots}{
29
-    \code{fontSize} is the size of the text labels of the nodes and the edges of the tree components. The default value is 8.
30
-    \code{k} is a \code{numeric} giving the specific tree component from the given mixture model that should be plotted. Its value 
31
-    can be from one to the number of tree components in the given model.
32
-  }
33
-}
34
-\value{
35
-  The method returns a plot of the mixture model model.
36
-}
37
-
38
-\references{Learning multiple evolutionary pathways from cross-sectional
39
-  data, N. Beerenwinkel et al.}
40
-
41
-\author{Jasmina Bogojeska}
42
- 
43
-\seealso{
44
-  \code{\link{RtreemixData-class}}, \code{\link{RtreemixModel-class}},
45
-  \code{\link{generate-methods}}
46
-}
47
-
48
-\examples{
49
-## Generate a random RtreemixModel object.
50
-rand.mod <- generate(K = 2, no.events = 7, noise.tree = TRUE, prob = c(0.2, 0.8))
51
-
52
-## Visualize it.
53
-plot(rand.mod)
54
-
55
-## Increase the font size of the text labels in the plot.
56
-plot(rand.mod, fontSize = 10)
57
-
58
-## Plot the second component of the mixture model rand.mod
59
-plot(rand.mod, k = 2)
60
-
61
-}
62
-
63
-\keyword{methods}