sCompReorder: Function to reorder component planes

Description Usage Arguments Value Note See Also Examples

View source: R/sCompReorder.r

Description

sCompReorder is supposed to reorder component planes for the input map/data. It returns an object of class "sReorder". It is realized by using a new map grid (with sheet shape consisting of a rectangular lattice) to train component plane vectors (either column-wise vectors of codebook/data matrix or the covariance matrix thereof). As a result, similar component planes are placed closer to each other. It is highly recommend to use trained map (i.e. codebook matrix) as input if data matrix is hugely big to save computational costs.

Usage

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sCompReorder(
sMap,
xdim = NULL,
ydim = NULL,
amplifier = NULL,
metric = c("none", "pearson", "spearman", "kendall", "euclidean",
"manhattan", "cos",
"mi"),
init = c("linear", "uniform", "sample"),
seed = 825,
algorithm = c("sequential", "batch"),
alphaType = c("invert", "linear", "power"),
neighKernel = c("gaussian", "bubble", "cutgaussian", "ep", "gamma"),
finetuneSustain = TRUE
)

Arguments

sMap

an object of class "sMap" or input data frame/matrix

xdim

an integer specifying x-dimension of the grid

ydim

an integer specifying y-dimension of the grid

amplifier

an integer specifying the amplifier (3 by default) of the number of component planes. The product of the component number and the amplifier constitutes the number of rectangles in the sheet grid

metric

distance metric used to define the similarity between component planes. It can be "none", which means directly using column-wise vectors of codebook/data matrix. Otherwise, first calculate the covariance matrix from the codebook/data matrix. The distance metric used for calculating the covariance matrix between component planes can be: "pearson" for pearson correlation, "spearman" for spearman rank correlation, "kendall" for kendall tau rank correlation, "euclidean" for euclidean distance, "manhattan" for cityblock distance, "cos" for cosine similarity, "mi" for mutual information. See sDistance for details

init

an initialisation method. It can be one of "uniform", "sample" and "linear" initialisation methods

seed

an integer specifying the seed

algorithm

the training algorithm. It can be one of "sequential" and "batch" algorithm. By default, it uses 'sequential' algorithm. If the input data contains a large number of samples but not a great amount of zero entries, then it is reasonable to use 'batch' algorithm for its fast computations (probably also without the compromise of accuracy)

alphaType

the alpha type. It can be one of "invert", "linear" and "power" alpha types

neighKernel

the training neighbor kernel. It can be one of "gaussian", "bubble", "cutgaussian", "ep" and "gamma" kernels

finetuneSustain

logical to indicate whether sustain the "finetune" training. If true, it will repeat the "finetune" stage until the mean quantization error does get worse. By default, it sets to TRUE

Value

an object of class "sReorder", a list with following components:

Note

All component planes are uniquely placed within a "sheet"-shape rectangle grid:

The size of "sheet"-shape rectangle grid depends on the input arguments:

See Also

sTopology, sPipeline, sBMH, sDistance, visCompReorder

Examples

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# 1) generate an iid normal random matrix of 100x10 
data <- matrix( rnorm(100*10,mean=0,sd=1), nrow=100, ncol=10)
colnames(data) <- paste(rep('S',10), seq(1:10), sep="")

# 2) get trained using by default setup
sMap <- sPipeline(data=data)

# 3) reorder component planes in different ways
# 3a) directly using column-wise vectors of codebook matrix
sReorder <- sCompReorder(sMap=sMap, amplifier=2, metric="none")
# 3b) according to covariance matrix of pearson correlation of codebook matrix
sReorder <- sCompReorder(sMap=sMap, amplifier=2, metric="pearson")
# 3c) according to covariance matrix of pearson correlation of input matrix
sReorder <- sCompReorder(sMap=data, amplifier=2, metric="pearson")

hfang-bristol/supraHex documentation built on May 24, 2021, 3:13 p.m.