Get Clustering Results for CBASS

Source: R/accessors_cbass.R

get_cluster_labels returns a factor vector of cluster labels. get_cluster_centroids returns a k1-by-k2 matrix with the estimated centroid of the k1-th row cluster and the k2-th column cluster. get_clustered_data returns a matrix (with the same dimensions and names as the original data), but with the values for each row replaced by its "estimated" value (i.e., the appropriate cluster centroid).

# S3 method for CBASS
get_cluster_labels(x, ..., percent, k.row, k.col, type = c("row", "col"))

# S3 method for CBASS
get_cluster_centroids(x, ..., percent, k.row, k.col, refit = TRUE)

# S3 method for CBASS
get_clustered_data(x, ..., percent, k.row, k.col, refit = TRUE)

Arguments

x

An object of class CARP as produced by CBASS
...

Additional arguments - if any are provided, an error is signalled.
percent

A number between 0 and 1, giving the regularization level (as a fraction of the final regularization level used) at which to get cluster labels.
k.row

The desired number of row clusters
k.col

The desired number of column clusters
type

For get_cluster_labels, which set of labels to return - row (observation) or column (feature)
refit

Should "naive" centroids (TRUE) or the actual centroids estimated by convex clustering be used? The default (refit = TRUE) centroids returned are actual centroids (mean) of all elements assigned to that cluster; if refit = FALSE, the \(\hat{U}\) from the convex biclustering problem is used. Due to the global shrinkage imposed, these clusters are more "shrunk together" than the naive clusters.

Details

get_clustered_data returns centroids on the original scale of the data, independent of any pre-processing flags passed to CBASS. Note that exactly one of percent, k.row, k.col must be supplied and that that k.row (if suppplied) will be used even if type = "col" and vice versa.

Examples

cbass_fit <- CBASS(presidential_speech)
#> Pre-computing column weights and edge sets
#> Pre-computing row weights and edge sets
#> Computing Convex Bi-Clustering [CBASS] Path
#> Post-processing rows
#> Post-processing columns

# Get row clustering results from 50% along the path
get_cluster_labels(cbass_fit, percent = 0.5)
#>        Abraham Lincoln         Andrew Jackson         Andrew Johnson 
#>              cluster_1              cluster_1              cluster_1 
#>           Barack Obama      Benjamin Harrison        Calvin Coolidge 
#>              cluster_2              cluster_1              cluster_1 
#>      Chester A. Arthur        Donald J. Trump   Dwight D. Eisenhower 
#>              cluster_1              cluster_2              cluster_2 
#>  Franklin D. Roosevelt        Franklin Pierce            George Bush 
#>              cluster_2              cluster_1              cluster_2 
#>         George W. Bush      George Washington         Gerald R. Ford 
#>              cluster_2              cluster_1              cluster_2 
#>       Grover Cleveland        Harry S. Truman         Herbert Hoover 
#>              cluster_1              cluster_2              cluster_1 
#>      James A. Garfield         James Buchanan          James K. Polk 
#>              cluster_1              cluster_1              cluster_1 
#>          James Madison           James Monroe           Jimmy Carter 
#>              cluster_1              cluster_1              cluster_2 
#>             John Adams        John F. Kennedy      John Quincy Adams 
#>              cluster_1              cluster_2              cluster_1 
#>             John Tyler      Lyndon B. Johnson       Martin van Buren 
#>              cluster_1              cluster_2              cluster_1 
#>       Millard Fillmore          Richard Nixon          Ronald Reagan 
#>              cluster_1              cluster_2              cluster_2 
#>    Rutherford B. Hayes     Theodore Roosevelt       Thomas Jefferson 
#>              cluster_1              cluster_1              cluster_1 
#>       Ulysses S. Grant      Warren G. Harding William Henry Harrison 
#>              cluster_1              cluster_1              cluster_1 
#>    William Howard Taft     William J. Clinton       William McKinley 
#>              cluster_1              cluster_2              cluster_1 
#>         Woodrow Wilson         Zachary Taylor 
#>              cluster_1              cluster_1 
#> Levels: cluster_1 cluster_2

# Get column clustering corresponding to the 3 cluster solution
get_cluster_labels(cbass_fit, k.col = 3, type = "col")
#>     amount   appropri    british       cent   commerci commission   consider 
#>  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1 
#>    develop expenditur       farm      feder     fiscal       help     indian 
#>  cluster_2  cluster_1  cluster_2  cluster_2  cluster_1  cluster_2  cluster_1 
#> intercours     island       june       mail     mexico       navi       need 
#>  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1  cluster_2 
#>        per     provis    receipt     reform     regard     report      shall 
#>  cluster_1  cluster_1  cluster_1  cluster_2  cluster_1  cluster_1  cluster_1 
#>    subject  territori   treasuri     treati       upon     vessel    america 
#>  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1  cluster_1  cluster_2 
#>       bank      incom    million      price      spain     articl        cut 
#>  cluster_1  cluster_2  cluster_2  cluster_1  cluster_1  cluster_1  cluster_3 
#>     dollar     econom      women       educ     school       bill     tariff 
#>  cluster_2  cluster_2  cluster_3  cluster_2  cluster_2  cluster_2  cluster_1 
#>   unemploy     weapon        get     method     farmer   challeng     achiev 
#>  cluster_3  cluster_3  cluster_3  cluster_2  cluster_2  cluster_3  cluster_2 
#>  democraci       area    billion    problem      basic     budget       goal 
#>  cluster_3  cluster_2  cluster_3  cluster_2  cluster_3  cluster_3  cluster_3 
#>        job      level    nuclear    percent    program      spend  technolog 
#>  cluster_3  cluster_3  cluster_3  cluster_3  cluster_3  cluster_3  cluster_3 
#>      today    tonight     worker     inflat     soviet 
#>  cluster_3  cluster_3  cluster_3  cluster_3  cluster_3 
#> Levels: cluster_1 cluster_2 cluster_3

# Get row clustering corresponding to the 3 column clusters
get_cluster_labels(cbass_fit, k.col = 3, type = "row")
#>        Abraham Lincoln         Andrew Jackson         Andrew Johnson 
#>              cluster_1              cluster_1              cluster_1 
#>           Barack Obama      Benjamin Harrison        Calvin Coolidge 
#>              cluster_2              cluster_1              cluster_1 
#>      Chester A. Arthur        Donald J. Trump   Dwight D. Eisenhower 
#>              cluster_1              cluster_2              cluster_2 
#>  Franklin D. Roosevelt        Franklin Pierce            George Bush 
#>              cluster_2              cluster_1              cluster_2 
#>         George W. Bush      George Washington         Gerald R. Ford 
#>              cluster_2              cluster_1              cluster_2 
#>       Grover Cleveland        Harry S. Truman         Herbert Hoover 
#>              cluster_1              cluster_2              cluster_1 
#>      James A. Garfield         James Buchanan          James K. Polk 
#>              cluster_1              cluster_1              cluster_1 
#>          James Madison           James Monroe           Jimmy Carter 
#>              cluster_1              cluster_1              cluster_2 
#>             John Adams        John F. Kennedy      John Quincy Adams 
#>              cluster_1              cluster_2              cluster_1 
#>             John Tyler      Lyndon B. Johnson       Martin van Buren 
#>              cluster_1              cluster_2              cluster_1 
#>       Millard Fillmore          Richard Nixon          Ronald Reagan 
#>              cluster_1              cluster_2              cluster_2 
#>    Rutherford B. Hayes     Theodore Roosevelt       Thomas Jefferson 
#>              cluster_1              cluster_1              cluster_1 
#>       Ulysses S. Grant      Warren G. Harding William Henry Harrison 
#>              cluster_1              cluster_1              cluster_1 
#>    William Howard Taft     William J. Clinton       William McKinley 
#>              cluster_1              cluster_2              cluster_1 
#>         Woodrow Wilson         Zachary Taylor 
#>              cluster_1              cluster_1 
#> Levels: cluster_1 cluster_2

# Get cluster centroids partially down the path
get_cluster_centroids(cbass_fit, percent = 0.5)
#>          [,1]     [,2]      [,3]
#> [1,] 2.778695 1.599787 0.3032325
#> [2,] 1.300215 3.396630 3.1146839

# Get clustered data
image(get_clustered_data(cbass_fit, k.row = 2))