cluster.sizestat: generate statistics on sizes of clusters
In ChemmineR: Cheminformatics Toolkit for R
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
'cluster.sizestat' is used to do simple statistics on sizes of clusters
generated by 'cmp.cluster'. It will return a dataframe which maps a cluster
size to the number of clusters with that size. It is often used along
with 'cluster.visualize'.
Usage
1
cluster.sizestat(cls, cluster.result=1)
Arguments
cls
The clustering result returned by 'cmp.cluster'
cluster.result
If multiple cutoff values are used in clustering process, this argument tells which cutoff value is to be considered here.
Details
'cluster.sizestat' depends on the format that is returned by 'cmp.cluster' - it
will treat the first column as the indecies, and the second column as the
cluster sizes of effective clustering. Because of this, when multiple
cutoffs are used when 'cmp.cluster' is called, 'cluster.sizestat' will only
consider the clustering result of the first cutoff. If you want to work on
an alternative cutoff, you have to manually reorder/remove columns.
Value
Returns a data frame of two columns.
cluster size
This column lists cluster sizes
count
This column lists number of clusters of a cluster size
Author(s)
Y. Eddie Cao
See Also
cmp.cluster, cluster.visualize
Examples
1
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## Load sample SD file
# data(sdfsample); sdfset <- sdfsample
## Generate atom pair descriptor database for searching
# apset <- sdf2ap(sdfset)
## Loads same atom pair sample data set provided by library
data(apset)
## Binning clustering using variable similarity cutoffs.
cluster <- cmp.cluster(db=apset, cutoff = c(0.65, 0.5))
## Statistics on sizes of clusters
cluster.sizestat(cluster[,c(1,2,3)])
cluster.sizestat(cluster[,c(1,4,5)])
Example output
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sorting result...
cluster size count
1 1 90
2 2 5
cluster size count
1 1 80
2 2 10
ChemmineR documentation built on Feb. 28, 2021, 2:02 a.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
'cluster.sizestat' is used to do simple statistics on sizes of clusters generated by 'cmp.cluster'. It will return a dataframe which maps a cluster size to the number of clusters with that size. It is often used along with 'cluster.visualize'.
Usage
1 | cluster.sizestat(cls, cluster.result=1)
|
Arguments
cls |
The clustering result returned by 'cmp.cluster' |
cluster.result |
If multiple cutoff values are used in clustering process, this argument tells which cutoff value is to be considered here. |
Details
'cluster.sizestat' depends on the format that is returned by 'cmp.cluster' - it will treat the first column as the indecies, and the second column as the cluster sizes of effective clustering. Because of this, when multiple cutoffs are used when 'cmp.cluster' is called, 'cluster.sizestat' will only consider the clustering result of the first cutoff. If you want to work on an alternative cutoff, you have to manually reorder/remove columns.
Value
Returns a data frame of two columns.
cluster size |
This column lists cluster sizes |
count |
This column lists number of clusters of a cluster size |
Author(s)
Y. Eddie Cao
See Also
cmp.cluster, cluster.visualize
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## Load sample SD file
# data(sdfsample); sdfset <- sdfsample
## Generate atom pair descriptor database for searching
# apset <- sdf2ap(sdfset)
## Loads same atom pair sample data set provided by library
data(apset)
## Binning clustering using variable similarity cutoffs.
cluster <- cmp.cluster(db=apset, cutoff = c(0.65, 0.5))
## Statistics on sizes of clusters
cluster.sizestat(cluster[,c(1,2,3)])
cluster.sizestat(cluster[,c(1,4,5)])
|
Example output
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/ 0 %
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/ 48 %
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\ 48 %
|
/ 49 %
-
\ 49 %
| 50 %
sorting result...
cluster size count
1 1 90
2 2 5
cluster size count
1 1 80
2 2 10
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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