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Spatial Convex Clustering

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PlotCV: A function for plotting cross validation errors

PlotCV: A function for plotting cross validation errors
In SpaCCr: Spatial Convex Clustering

Description Usage Arguments Examples

Description

A function for plotting cross validation errors

Usage

1
PlotCV(ErrMat, rule = 2, gamma.seq)

Arguments

ErrMat

A matrix of error outputted by SpaCC_CV

rule

An interger indicating which CV rule to choose

gamma.seq

The sequence of regularization parameters

Examples

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library(dplyr)
library(tidyr)
data("methy")
methy <- methy[1:20,1:10]
Coordinates <- methy$Genomic_Coordinate
methy %>%
 tbl_df() %>%
 select(-Chromosome,-Genomic_Coordinate) %>%
 gather(Subject,Value,-ProbeID) %>%
 spread(ProbeID,Value) -> X
SubjectLabels <- X$Subject
X <- X[,-1] %>% as.matrix()
nsubj <- nrow(X)
nprobes <- ncol(X)
nweights <- choose(nprobes,2)
diff.vals <- diff(Coordinates)
too.far <- diff.vals > 20000
sig = 1/5e3
w.values <- exp(-sig*diff.vals)
w.values[too.far] = 0

verbose=TRUE
tol.base = 1e-4
tol.miss = 1e-4
max.iter.base=5000
max.iter.miss=500
ngam = 20
gamma.seq <- exp(seq(log(1e-1),log(1e1),length.out=ngam))
CVRes <- SpaCC_CV(X=t(scale(t(X),center=TRUE,scale=FALSE)),
                 w=w.values,
                 gamma.seq=gamma.seq,
                 nfolds=5,
                 nu=1/nsubj,
                 verbose=TRUE,
                 tol.base=tol.base,
                 tol.miss=tol.miss,
                 max.iter.base=max.iter.base,
                 max.iter.miss=max.iter.miss,
                 parallel=FALSE,frac = 1)
PlotCV(CVRes$ErrMat,gamma.seq = CVRes$gamma.seq,rule = 1)

Example output

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

[1] "Fold # 1 of 5"
[1] "Solving Path Problem 36"
[1] "gamma iter is: 1"
[1] "Miss Iter 183"
[1] "Missing Error: 9.96420632428748e-05"
[1] "gamma iter is: 2"
[1] "Miss Iter 172"
[1] "Missing Error: 9.87893963937968e-05"
[1] "gamma iter is: 3"
[1] "Miss Iter 257"
[1] "Missing Error: 9.91332187129847e-05"
[1] "gamma iter is: 4"
[1] "Miss Iter 227"
[1] "Missing Error: 9.89122934604162e-05"
[1] "gamma iter is: 5"
[1] "Miss Iter 173"
[1] "Missing Error: 9.98133925859917e-05"
[1] "gamma iter is: 6"
[1] "Miss Iter 135"
[1] "Missing Error: 9.97704753529657e-05"
[1] "gamma iter is: 7"
[1] "Miss Iter 112"
[1] "Missing Error: 9.81848399565797e-05"
[1] "gamma iter is: 8"
[1] "Miss Iter 52"
[1] "Missing Error: 9.976468977299e-05"
[1] "gamma iter is: 9"
[1] "Miss Iter 31"
[1] "Missing Error: 9.2461467128216e-05"
[1] "gamma iter is: 10"
[1] "Miss Iter 39"
[1] "Missing Error: 9.96350117689432e-05"
[1] "gamma iter is: 11"
[1] "Miss Iter 33"
[1] "Missing Error: 9.59706725212691e-05"
[1] "gamma iter is: 12"
[1] "Miss Iter 28"
[1] "Missing Error: 8.92413981383739e-05"
[1] "gamma iter is: 13"
[1] "Miss Iter 31"
[1] "Missing Error: 8.12841167133782e-05"
[1] "gamma iter is: 14"
[1] "Miss Iter 27"
[1] "Missing Error: 8.16229170941841e-05"
[1] "gamma iter is: 15"
[1] "Miss Iter 38"
[1] "Missing Error: 9.64515679479335e-05"
[1] "gamma iter is: 16"
[1] "Miss Iter 47"
[1] "Missing Error: 9.16514777160457e-05"
[1] "gamma iter is: 17"
[1] "Miss Iter 58"
[1] "Missing Error: 9.42974035899028e-05"
[1] "gamma iter is: 18"
[1] "Miss Iter 70"
[1] "Missing Error: 9.77400055483119e-05"
[1] "gamma iter is: 19"
[1] "Miss Iter 84"
[1] "Missing Error: 9.83842328927673e-05"
[1] "gamma iter is: 20"
[1] "Miss Iter 103"
[1] "Missing Error: 9.91980552476925e-05"
[1] "Computing Error"
[1] "Fold # 2 of 5"
[1] "Solving Path Problem 21"
[1] "gamma iter is: 1"
[1] "Miss Iter 327"
[1] "Missing Error: 9.9410602696753e-05"
[1] "gamma iter is: 2"
[1] "Miss Iter 323"
[1] "Missing Error: 9.96105993737349e-05"
[1] "gamma iter is: 3"
[1] "Miss Iter 332"
[1] "Missing Error: 9.94264203286238e-05"
[1] "gamma iter is: 4"
[1] "Miss Iter 327"
[1] "Missing Error: 9.90268345499751e-05"
[1] "gamma iter is: 5"
[1] "Miss Iter 264"
[1] "Missing Error: 9.96645129302052e-05"
[1] "gamma iter is: 6"
[1] "Miss Iter 239"
[1] "Missing Error: 9.8962859160257e-05"
[1] "gamma iter is: 7"
[1] "Miss Iter 140"
[1] "Missing Error: 9.88213753156799e-05"
[1] "gamma iter is: 8"
[1] "Miss Iter 77"
[1] "Missing Error: 9.95668709630333e-05"
[1] "gamma iter is: 9"
[1] "Miss Iter 38"
[1] "Missing Error: 9.56457077550395e-05"
[1] "gamma iter is: 10"
[1] "Miss Iter 36"
[1] "Missing Error: 9.93057107914262e-05"
[1] "gamma iter is: 11"
[1] "Miss Iter 34"
[1] "Missing Error: 9.9521802115562e-05"
[1] "gamma iter is: 12"
[1] "Miss Iter 30"
[1] "Missing Error: 8.1739256554307e-05"
[1] "gamma iter is: 13"
[1] "Miss Iter 26"
[1] "Missing Error: 9.28246975111266e-05"
[1] "gamma iter is: 14"
[1] "Miss Iter 26"
[1] "Missing Error: 9.88420546758231e-05"
[1] "gamma iter is: 15"
[1] "Miss Iter 31"
[1] "Missing Error: 8.83464715322873e-05"
[1] "gamma iter is: 16"
[1] "Miss Iter 40"
[1] "Missing Error: 9.61350182488027e-05"
[1] "gamma iter is: 17"
[1] "Miss Iter 51"
[1] "Missing Error: 9.8894809724425e-05"
[1] "gamma iter is: 18"
[1] "Miss Iter 64"
[1] "Missing Error: 9.79890352026844e-05"
[1] "gamma iter is: 19"
[1] "Miss Iter 79"
[1] "Missing Error: 9.83383361702676e-05"
[1] "gamma iter is: 20"
[1] "Miss Iter 97"
[1] "Missing Error: 9.67652293263456e-05"
[1] "Computing Error"
[1] "Fold # 3 of 5"
[1] "Solving Path Problem 23"
[1] "gamma iter is: 1"
[1] "Miss Iter 230"
[1] "Missing Error: 9.90370667016967e-05"
[1] "gamma iter is: 2"
[1] "Miss Iter 211"
[1] "Missing Error: 9.93586256597732e-05"
[1] "gamma iter is: 3"
[1] "Miss Iter 203"
[1] "Missing Error: 9.99417500744001e-05"
[1] "gamma iter is: 4"
[1] "Miss Iter 185"
[1] "Missing Error: 9.99719681928203e-05"
[1] "gamma iter is: 5"
[1] "Miss Iter 154"
[1] "Missing Error: 9.82673804900589e-05"
[1] "gamma iter is: 6"
[1] "Miss Iter 96"
[1] "Missing Error: 9.80092726245606e-05"
[1] "gamma iter is: 7"
[1] "Miss Iter 90"
[1] "Missing Error: 9.82041474433207e-05"
[1] "gamma iter is: 8"
[1] "Miss Iter 46"
[1] "Missing Error: 9.82604935514865e-05"
[1] "gamma iter is: 9"
[1] "Miss Iter 29"
[1] "Missing Error: 9.88344131187884e-05"
[1] "gamma iter is: 10"
[1] "Miss Iter 45"
[1] "Missing Error: 9.83752840030116e-05"
[1] "gamma iter is: 11"
[1] "Miss Iter 37"
[1] "Missing Error: 9.75948157452918e-05"
[1] "gamma iter is: 12"
[1] "Miss Iter 37"
[1] "Missing Error: 8.12691326133834e-05"
[1] "gamma iter is: 13"
[1] "Miss Iter 37"
[1] "Missing Error: 9.28698095573254e-05"
[1] "gamma iter is: 14"
[1] "Miss Iter 28"
[1] "Missing Error: 8.63623971791219e-05"
[1] "gamma iter is: 15"
[1] "Miss Iter 29"
[1] "Missing Error: 7.74367690183461e-05"
[1] "gamma iter is: 16"
[1] "Miss Iter 37"
[1] "Missing Error: 9.12376391087031e-05"
[1] "gamma iter is: 17"
[1] "Miss Iter 48"
[1] "Missing Error: 9.05809409867083e-05"
[1] "gamma iter is: 18"
[1] "Miss Iter 60"
[1] "Missing Error: 9.61311878159113e-05"
[1] "gamma iter is: 19"
[1] "Miss Iter 75"
[1] "Missing Error: 9.46193449080903e-05"
[1] "gamma iter is: 20"
[1] "Miss Iter 92"
[1] "Missing Error: 9.68245270161788e-05"
[1] "Computing Error"
[1] "Fold # 4 of 5"
[1] "Solving Path Problem 29"
[1] "gamma iter is: 1"
[1] "Miss Iter 184"
[1] "Missing Error: 9.84663708694612e-05"
[1] "gamma iter is: 2"
[1] "Miss Iter 141"
[1] "Missing Error: 9.98868296099149e-05"
[1] "gamma iter is: 3"
[1] "Miss Iter 181"
[1] "Missing Error: 9.93759588991182e-05"
[1] "gamma iter is: 4"
[1] "Miss Iter 139"
[1] "Missing Error: 9.95585772130624e-05"
[1] "gamma iter is: 5"
[1] "Miss Iter 141"
[1] "Missing Error: 9.91512834303379e-05"
[1] "gamma iter is: 6"
[1] "Miss Iter 103"
[1] "Missing Error: 9.96473728028223e-05"
[1] "gamma iter is: 7"
[1] "Miss Iter 70"
[1] "Missing Error: 9.95143454478083e-05"
[1] "gamma iter is: 8"
[1] "Miss Iter 63"
[1] "Missing Error: 9.76286429051151e-05"
[1] "gamma iter is: 9"
[1] "Miss Iter 40"
[1] "Missing Error: 9.88033405342453e-05"
[1] "gamma iter is: 10"
[1] "Miss Iter 45"
[1] "Missing Error: 9.3130133111294e-05"
[1] "gamma iter is: 11"
[1] "Miss Iter 44"
[1] "Missing Error: 9.41747619112116e-05"
[1] "gamma iter is: 12"
[1] "Miss Iter 37"
[1] "Missing Error: 7.81152404392269e-05"
[1] "gamma iter is: 13"
[1] "Miss Iter 31"
[1] "Missing Error: 7.8748710828351e-05"
[1] "gamma iter is: 14"
[1] "Miss Iter 27"
[1] "Missing Error: 7.96200235370102e-05"
[1] "gamma iter is: 15"
[1] "Miss Iter 29"
[1] "Missing Error: 9.21458542762639e-05"
[1] "gamma iter is: 16"
[1] "Miss Iter 45"
[1] "Missing Error: 9.13561299575806e-05"
[1] "gamma iter is: 17"
[1] "Miss Iter 61"
[1] "Missing Error: 9.28013142872468e-05"
[1] "gamma iter is: 18"
[1] "Miss Iter 78"
[1] "Missing Error: 9.74743010383988e-05"
[1] "gamma iter is: 19"
[1] "Miss Iter 98"
[1] "Missing Error: 9.71012459700657e-05"
[1] "gamma iter is: 20"
[1] "Miss Iter 120"
[1] "Missing Error: 9.91368356127206e-05"
[1] "Computing Error"
[1] "Fold # 5 of 5"
[1] "Solving Path Problem 31"
[1] "gamma iter is: 1"
[1] "Miss Iter 195"
[1] "Missing Error: 9.97156741334859e-05"
[1] "gamma iter is: 2"
[1] "Miss Iter 209"
[1] "Missing Error: 9.98470999337443e-05"
[1] "gamma iter is: 3"
[1] "Miss Iter 202"
[1] "Missing Error: 9.88834123225377e-05"
[1] "gamma iter is: 4"
[1] "Miss Iter 196"
[1] "Missing Error: 9.86938632520866e-05"
[1] "gamma iter is: 5"
[1] "Miss Iter 190"
[1] "Missing Error: 9.85317735874559e-05"
[1] "gamma iter is: 6"
[1] "Miss Iter 149"
[1] "Missing Error: 9.81623120355723e-05"
[1] "gamma iter is: 7"
[1] "Miss Iter 91"
[1] "Missing Error: 9.91120105655017e-05"
[1] "gamma iter is: 8"
[1] "Miss Iter 37"
[1] "Missing Error: 9.78296589862601e-05"
[1] "gamma iter is: 9"
[1] "Miss Iter 49"
[1] "Missing Error: 9.91002581960408e-05"
[1] "gamma iter is: 10"
[1] "Miss Iter 32"
[1] "Missing Error: 9.54711167351099e-05"
[1] "gamma iter is: 11"
[1] "Miss Iter 28"
[1] "Missing Error: 9.60161540548048e-05"
[1] "gamma iter is: 12"
[1] "Miss Iter 32"
[1] "Missing Error: 8.17619824004549e-05"
[1] "gamma iter is: 13"
[1] "Miss Iter 30"
[1] "Missing Error: 9.47124648947996e-05"
[1] "gamma iter is: 14"
[1] "Miss Iter 35"
[1] "Missing Error: 8.92789198468544e-05"
[1] "gamma iter is: 15"
[1] "Miss Iter 49"
[1] "Missing Error: 9.84561410809663e-05"
[1] "gamma iter is: 16"
[1] "Miss Iter 65"
[1] "Missing Error: 9.6259419769719e-05"
[1] "gamma iter is: 17"
[1] "Miss Iter 83"
[1] "Missing Error: 9.52125776990568e-05"
[1] "gamma iter is: 18"
[1] "Miss Iter 102"
[1] "Missing Error: 9.92883380103905e-05"
[1] "gamma iter is: 19"
[1] "Miss Iter 125"
[1] "Missing Error: 9.77806890424049e-05"
[1] "gamma iter is: 20"
[1] "Miss Iter 150"
[1] "Missing Error: 9.89182098129655e-05"
[1] "Computing Error"

SpaCCr documentation built on May 2, 2019, 11:02 a.m.

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