Description Usage Arguments Details Value Author(s) See Also Examples
A visual comparison of all methods is handy to see which compounds will always
cluster together independent of the applied methods. The function CompareSvsM
plots the ComparePlot
of the single source clustering results on the left and
that of the multiple source clustering results on the right such that a visual
comparison is possible.
1 2 3 |
ListS |
A list of the outputs from the single source clusterings to be compared. The first element of the
list will be used as the reference in |
ListM |
A list of the outputs from the multiple source clusterings to be compared. The first element of the list will be used as the reference. |
nrclusters |
The number of clusters to cut the dendrogram in. |
cols |
The hex codes of the colors to be used. |
fusionsLogS |
The fusionslog parameter for the elements in ListS. To be handed to |
fusionsLogM |
The fusionsLog parameter for the elements in ListM. To be handed to |
WeightClustS |
The WeightClust parameter for the elements in ListS. To be handed to |
WeightClustM |
The WeightClust parameter for the elements in ListM. To be handed to |
namesS |
Optional. Names of the single source clusterings to be used as labels for the columns. |
namesM |
Optional. Names of the multiple source clusterings to be used as labels for the columns. |
margins |
Optional. Margins to be used for the plot. |
plottype |
Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document, i.e. no new device is opened and the plot appears in the current device or document. |
location |
If plottype is "pdf", a location should be provided in "location" and the figure is saved there. |
... |
Other options which can be given to the |
This function relies on ComparePlot
to plot both the results of the single source
clusterings as the multiple source clusterings.
The returned value is a plot with on the left the comparison over the objects in ListS and on the right a comparison over the objects in ListM.
Marijke Van Moerbeke
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | data(fingerprintMat)
data(targetMat)
data(Colors2)
MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
L=list(fingerprintMat,targetMat)
MCF7_W=WeightedClust(L,type="data", distmeasure=c("tanimoto","tanimoto"),normalize=FALSE,
method=NULL,weight=seq(1,0,-0.1),WeightClust=0.5,clust="agnes",linkage="ward",StopRange=FALSE)
ListM=list(MCF7_W)
namesM=seq(1.0,0.0,-0.1)
ListS=list(MCF7_F,MCF7_T)
namesS=c("FP","TP")
CompareSvsM(ListS,ListM,nrclusters=7,cols=Colors2,fusionsLogS=FALSE,
fusionsLogM=FALSE,WeightClustS=FALSE,WeightClustM=FALSE,namesS,
namesM,reverse=FALSE,plottype="new",location=NULL)
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