miga-base 0.4.3.0 → 0.5.0.0
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/README.md +1 -1
- data/lib/miga/cli.rb +43 -223
- data/lib/miga/cli/action/add.rb +91 -62
- data/lib/miga/cli/action/classify_wf.rb +97 -0
- data/lib/miga/cli/action/daemon.rb +14 -10
- data/lib/miga/cli/action/derep_wf.rb +95 -0
- data/lib/miga/cli/action/doctor.rb +83 -55
- data/lib/miga/cli/action/get.rb +68 -52
- data/lib/miga/cli/action/get_db.rb +206 -0
- data/lib/miga/cli/action/index_wf.rb +31 -0
- data/lib/miga/cli/action/init.rb +115 -190
- data/lib/miga/cli/action/init/daemon_helper.rb +124 -0
- data/lib/miga/cli/action/ls.rb +20 -11
- data/lib/miga/cli/action/ncbi_get.rb +199 -157
- data/lib/miga/cli/action/preproc_wf.rb +46 -0
- data/lib/miga/cli/action/quality_wf.rb +45 -0
- data/lib/miga/cli/action/stats.rb +147 -99
- data/lib/miga/cli/action/summary.rb +10 -4
- data/lib/miga/cli/action/tax_dist.rb +61 -46
- data/lib/miga/cli/action/tax_test.rb +46 -39
- data/lib/miga/cli/action/wf.rb +178 -0
- data/lib/miga/cli/base.rb +11 -0
- data/lib/miga/cli/objects_helper.rb +88 -0
- data/lib/miga/cli/opt_helper.rb +160 -0
- data/lib/miga/daemon.rb +7 -4
- data/lib/miga/dataset/base.rb +5 -5
- data/lib/miga/project/base.rb +4 -4
- data/lib/miga/project/result.rb +2 -1
- data/lib/miga/remote_dataset/base.rb +5 -5
- data/lib/miga/remote_dataset/download.rb +1 -1
- data/lib/miga/version.rb +3 -3
- data/scripts/cds.bash +3 -1
- data/scripts/essential_genes.bash +1 -0
- data/scripts/stats.bash +1 -1
- data/scripts/trimmed_fasta.bash +5 -3
- data/utils/distance/runner.rb +3 -0
- data/utils/distance/temporal.rb +10 -1
- data/utils/enveomics/Manifest/Tasks/fasta.json +5 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +7 -0
- data/utils/enveomics/Scripts/BlastTab.addlen.rb +33 -31
- data/utils/enveomics/Scripts/FastA.tag.rb +42 -41
- data/utils/enveomics/Scripts/HMM.essential.rb +85 -55
- data/utils/enveomics/Scripts/HMM.haai.rb +29 -20
- data/utils/enveomics/Scripts/SRA.download.bash +1 -1
- data/utils/enveomics/Scripts/aai.rb +163 -128
- data/utils/enveomics/build_enveomics_r.bash +11 -10
- data/utils/enveomics/enveomics.R/DESCRIPTION +3 -2
- data/utils/enveomics/enveomics.R/R/autoprune.R +141 -107
- data/utils/enveomics/enveomics.R/R/barplot.R +105 -86
- data/utils/enveomics/enveomics.R/R/cliopts.R +131 -115
- data/utils/enveomics/enveomics.R/R/df2dist.R +144 -106
- data/utils/enveomics/enveomics.R/R/growthcurve.R +201 -133
- data/utils/enveomics/enveomics.R/R/recplot.R +350 -315
- data/utils/enveomics/enveomics.R/R/recplot2.R +1334 -914
- data/utils/enveomics/enveomics.R/R/tribs.R +521 -361
- data/utils/enveomics/enveomics.R/R/utils.R +31 -15
- data/utils/enveomics/enveomics.R/README.md +7 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +16 -21
- data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +31 -28
- data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -19
- data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +36 -26
- data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -24
- data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -24
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +32 -33
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +91 -64
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +57 -37
- data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -19
- data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +39 -26
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +38 -25
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +40 -26
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +67 -49
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +37 -28
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +122 -97
- data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +35 -31
- data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -23
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +68 -51
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -24
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -22
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -20
- data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +41 -32
- data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -24
- data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -18
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +40 -34
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -24
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -20
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -20
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -29
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +41 -42
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -18
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +43 -33
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +36 -28
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +74 -56
- data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +44 -31
- data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -22
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +32 -26
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +59 -44
- data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -21
- data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -22
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +63 -43
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +38 -29
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +38 -30
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +111 -83
- data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -18
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -18
- data/utils/find-medoid.R +3 -2
- data/utils/representatives.rb +5 -3
- data/utils/subclade/pipeline.rb +22 -11
- data/utils/subclade/runner.rb +5 -1
- data/utils/subclades-compile.rb +1 -1
- data/utils/subclades.R +9 -3
- metadata +15 -4
- data/utils/enveomics/enveomics.R/man/enveomics.R-package.Rd +0 -15
- data/utils/enveomics/enveomics.R/man/z$-methods.Rd +0 -26
@@ -24,400 +24,560 @@
|
|
24
24
|
# ...
|
25
25
|
|
26
26
|
|
27
|
+
|
27
28
|
#==============> Define S4 classes
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
|
70
|
-
|
71
|
-
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
|
76
|
-
|
77
|
-
|
78
|
-
|
79
|
-
|
29
|
+
|
30
|
+
#' Enveomics: TRIBS S4 Class
|
31
|
+
#'
|
32
|
+
#' Enve-omics representation of "Transformed-space Resampling In Biased Sets
|
33
|
+
#' (TRIBS)". This object represents sets of distances between objects,
|
34
|
+
#' sampled nearly-uniformly at random in "distance space". Subsampling
|
35
|
+
#' without selection is trivial, since both the distances space and the
|
36
|
+
#' selection occur in the same transformed space. However, it's useful to
|
37
|
+
#' compare randomly subsampled sets against a selected set of objects. This
|
38
|
+
#' is intended to identify overdispersion or overclustering (see
|
39
|
+
#' \code{\link{enve.TRIBStest}}) of a subset against the entire collection of objects
|
40
|
+
#' with minimum impact of sampling biases. This object can be produced by
|
41
|
+
#' \code{\link{enve.tribs}} and supports S4 methods \code{plot} and \code{summary}.
|
42
|
+
#'
|
43
|
+
#' @slot distance \code{(numeric)} Centrality measurement of the distances
|
44
|
+
#' between the selected objects (without subsampling).
|
45
|
+
#' @slot points \code{(matrix)} Position of the different objects in distance
|
46
|
+
#' space.
|
47
|
+
#' @slot distances \code{(matrix)} Subsampled distances, where the rows are
|
48
|
+
#' replicates and the columns are subsampling levels.
|
49
|
+
#' @slot spaceSize \code{(numeric)} Number of objects.
|
50
|
+
#' @slot selSize \code{(numeric)} Number of selected objects.
|
51
|
+
#' @slot dimensions \code{(numeric)} Number of dimensions in the distance space.
|
52
|
+
#' @slot subsamples \code{(numeric)} Subsampling levels (as fractions, from
|
53
|
+
#' 0 to 1).
|
54
|
+
#' @slot call \code{(call)} Call producing this object.
|
55
|
+
#'
|
56
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
57
|
+
#'
|
58
|
+
#' @exportClass
|
59
|
+
|
60
|
+
enve.TRIBS <- setClass("enve.TRIBS",
|
61
|
+
representation(
|
62
|
+
distance='numeric',
|
63
|
+
points='matrix',
|
64
|
+
distances='matrix',
|
65
|
+
spaceSize='numeric',
|
66
|
+
selSize='numeric',
|
67
|
+
dimensions='numeric',
|
68
|
+
subsamples='numeric',
|
69
|
+
call='call')
|
70
|
+
,package='enveomics.R'
|
71
|
+
);
|
72
|
+
|
73
|
+
#' Enveomics: TRIBS Test S4 Class
|
74
|
+
#'
|
75
|
+
#' Test of significance of overclustering or overdispersion in a selected
|
76
|
+
#' set of objects with respect to the entire set (see \code{\link{enve.TRIBS}}). This
|
77
|
+
#' object can be produced by \code{\link{enve.tribs.test}} and supports S4 methods
|
78
|
+
#' \code{plot} and \code{summary}.
|
79
|
+
#'
|
80
|
+
#' @slot pval.gt \code{(numeric)}
|
81
|
+
#' P-value for the overdispersion test.
|
82
|
+
#' @slot pval.lt \code{(numeric)}
|
83
|
+
#' P-value for the overclustering test.
|
84
|
+
#' @slot all.dist \code{(numeric)}
|
85
|
+
#' Empiric PDF of distances for the entire dataset (subsampled at selection
|
86
|
+
#' size).
|
87
|
+
#' @slot sel.dist \code{(numeric)}
|
88
|
+
#' Empiric PDF of distances for the selected objects (without subsampling).
|
89
|
+
#' @slot diff.dist \code{(numeric)}
|
90
|
+
#' Empiric PDF of the difference between \code{all.dist} and \code{sel.dist}.
|
91
|
+
#' The p-values are estimating by comparing areas in this PDF greater than and
|
92
|
+
#' lesser than zero.
|
93
|
+
#' @slot dist.mids \code{(numeric)}
|
94
|
+
#' Midpoints of the empiric PDFs of distances.
|
95
|
+
#' @slot diff.mids \code{(numeric)}
|
96
|
+
#' Midpoints of the empiric PDF of difference of distances.
|
97
|
+
#' @slot call \code{(call)}
|
98
|
+
#' Call producing this object.
|
99
|
+
#'
|
100
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
101
|
+
#'
|
102
|
+
#' @exportClass
|
103
|
+
|
104
|
+
enve.TRIBStest <- setClass("enve.TRIBStest",
|
105
|
+
representation(
|
106
|
+
pval.gt='numeric',
|
107
|
+
pval.lt='numeric',
|
108
|
+
all.dist='numeric',
|
109
|
+
sel.dist='numeric',
|
110
|
+
diff.dist='numeric',
|
111
|
+
dist.mids='numeric',
|
112
|
+
diff.mids='numeric',
|
113
|
+
call='call')
|
114
|
+
,package='enveomics.R'
|
115
|
+
);
|
80
116
|
|
81
117
|
#==============> Define S4 methods
|
118
|
+
|
119
|
+
#' Enveomics: TRIBS Summary
|
120
|
+
#'
|
121
|
+
#' Summary of an \code{\link{enve.TRIBS}} object.
|
122
|
+
#'
|
123
|
+
#' @param object
|
124
|
+
#' \code{\link{enve.TRIBS}} object.
|
125
|
+
#' @param ...
|
126
|
+
#' No additional parameters are currently supported.
|
127
|
+
#'
|
128
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
129
|
+
#'
|
130
|
+
#' @method summary enve.TRIBS
|
131
|
+
#' @export
|
132
|
+
|
82
133
|
summary.enve.TRIBS <- function
|
83
|
-
|
84
|
-
|
85
|
-
|
86
|
-
|
87
|
-
|
88
|
-
){
|
89
|
-
cat('===[ enve.TRIBS ]-------------------------\n');
|
90
|
-
cat('Selected',attr(object,'selSize'),'of',
|
134
|
+
(object,
|
135
|
+
...
|
136
|
+
){
|
137
|
+
cat('===[ enve.TRIBS ]-------------------------\n');
|
138
|
+
cat('Selected',attr(object,'selSize'),'of',
|
91
139
|
attr(object,'spaceSize'),'objects in',
|
92
140
|
attr(object,'dimensions'),'dimensions.\n');
|
93
|
-
|
141
|
+
cat('Collected',length(attr(object,'subsamples')),'subsamples with',
|
94
142
|
nrow(attr(object,'distances')),'replicates each.\n');
|
95
|
-
|
96
|
-
|
97
|
-
|
143
|
+
cat('------------------------------------------\n');
|
144
|
+
cat('call:',as.character(attr(object,'call')),'\n');
|
145
|
+
cat('------------------------------------------\n');
|
98
146
|
}
|
99
147
|
|
148
|
+
#' Enveomics: TRIBS Plot
|
149
|
+
#'
|
150
|
+
#' Plot an \code{\link{enve.TRIBS}} object.
|
151
|
+
#'
|
152
|
+
#' @param x
|
153
|
+
#' \code{\link{enve.TRIBS}} object to plot.
|
154
|
+
#' @param new
|
155
|
+
#' Should a new canvas be drawn?
|
156
|
+
#' @param type
|
157
|
+
#' Type of plot. The \strong{points} plot shows all the replicates, the
|
158
|
+
#' \strong{boxplot} plot represents the values found by
|
159
|
+
#' \code{\link[grDevices]{boxplot.stats}}.
|
160
|
+
#' as areas, and plots the outliers as points.
|
161
|
+
#' @param col
|
162
|
+
#' Color of the areas and/or the points.
|
163
|
+
#' @param pt.cex
|
164
|
+
#' Size of the points.
|
165
|
+
#' @param pt.pch
|
166
|
+
#' Points character.
|
167
|
+
#' @param pt.col
|
168
|
+
#' Color of the points.
|
169
|
+
#' @param ln.col
|
170
|
+
#' Color of the lines.
|
171
|
+
#' @param ...
|
172
|
+
#' Any additional parameters supported by \code{plot}.
|
173
|
+
#'
|
174
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
175
|
+
#'
|
176
|
+
#' @method plot enve.TRIBS
|
177
|
+
#' @export
|
178
|
+
|
100
179
|
plot.enve.TRIBS <- function
|
101
|
-
|
102
|
-
|
103
|
-
|
104
|
-
|
105
|
-
|
106
|
-
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
|
112
|
-
|
113
|
-
|
114
|
-
|
115
|
-
|
116
|
-
|
117
|
-
|
118
|
-
|
119
|
-
|
120
|
-
|
121
|
-
|
122
|
-
|
123
|
-
|
124
|
-
|
125
|
-
|
126
|
-
|
127
|
-
|
128
|
-
|
129
|
-
|
130
|
-
|
131
|
-
|
132
|
-
|
133
|
-
|
134
|
-
|
135
|
-
|
136
|
-
for(i in 1:ncol(attr(x,'distances'))){
|
137
|
-
b <- boxplot.stats(attr(x,'distances')[,i]);
|
138
|
-
points(rep(round(attr(x,'subsamples')[i]*attr(x,'selSize')),
|
139
|
-
length(b$out)), b$out, cex=pt.cex, pch=pt.pch, col=pt.col);
|
140
|
-
stats[, i] <- c(b$conf, b$stats[c(1,5,2,4,3)]);
|
141
|
-
}
|
142
|
-
x <- round(attr(x,'subsamples')*attr(x,'selSize'))
|
143
|
-
for(i in c(1,3,5))
|
144
|
-
polygon(c(x, rev(x)), c(stats[i,], rev(stats[i+1,])), border=NA,
|
145
|
-
col=col);
|
146
|
-
lines(x, stats[7,], col=ln.col, lwd=2);
|
147
|
-
}
|
180
|
+
(x,
|
181
|
+
new=TRUE,
|
182
|
+
type=c('boxplot', 'points'),
|
183
|
+
col='#00000044',
|
184
|
+
pt.cex=1/2,
|
185
|
+
pt.pch=19,
|
186
|
+
pt.col=col,
|
187
|
+
ln.col=col,
|
188
|
+
...
|
189
|
+
){
|
190
|
+
type <- match.arg(type);
|
191
|
+
plot.opts <- list(xlim=range(attr(x,'subsamples'))*attr(x,'selSize'),
|
192
|
+
ylim=range(attr(x,'distances')), ..., t='n', x=1);
|
193
|
+
if(new) do.call(plot, plot.opts);
|
194
|
+
abline(h=attr(x,'distance'), lty=3, col=ln.col);
|
195
|
+
replicates <- nrow(attr(x,'distances'));
|
196
|
+
if(type=='points'){
|
197
|
+
for(i in 1:ncol(attr(x,'distances')))
|
198
|
+
points(rep(round(attr(x,'subsamples')[i]*attr(x,'selSize')),
|
199
|
+
replicates), attr(x,'distances')[,i], cex=pt.cex, pch=pt.pch,
|
200
|
+
col=pt.col);
|
201
|
+
}else{
|
202
|
+
stats <- matrix(NA, nrow=7, ncol=ncol(attr(x,'distances')));
|
203
|
+
for(i in 1:ncol(attr(x,'distances'))){
|
204
|
+
b <- boxplot.stats(attr(x,'distances')[,i]);
|
205
|
+
points(rep(round(attr(x,'subsamples')[i]*attr(x,'selSize')),
|
206
|
+
length(b$out)), b$out, cex=pt.cex, pch=pt.pch, col=pt.col);
|
207
|
+
stats[, i] <- c(b$conf, b$stats[c(1,5,2,4,3)]);
|
208
|
+
}
|
209
|
+
x <- round(attr(x,'subsamples')*attr(x,'selSize'))
|
210
|
+
for(i in c(1,3,5))
|
211
|
+
polygon(c(x, rev(x)), c(stats[i,], rev(stats[i+1,])), border=NA,
|
212
|
+
col=col);
|
213
|
+
lines(x, stats[7,], col=ln.col, lwd=2);
|
214
|
+
}
|
148
215
|
}
|
149
216
|
|
217
|
+
#' Enveomics: TRIBS Summary Test
|
218
|
+
#'
|
219
|
+
#' Summary of an \code{\link{enve.TRIBStest}} object.
|
220
|
+
#'
|
221
|
+
#' @param object
|
222
|
+
#' \code{\link{enve.TRIBStest}} object.
|
223
|
+
#' @param ...
|
224
|
+
#' No additional parameters are currently supported.
|
225
|
+
#'
|
226
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
227
|
+
#'
|
228
|
+
#' @method summary enve.TRIBStest
|
229
|
+
#' @export
|
230
|
+
|
150
231
|
summary.enve.TRIBStest <- function
|
151
|
-
|
152
|
-
|
153
|
-
|
154
|
-
|
155
|
-
|
156
|
-
)
|
157
|
-
|
158
|
-
|
159
|
-
|
160
|
-
|
161
|
-
|
162
|
-
|
163
|
-
|
164
|
-
|
165
|
-
|
166
|
-
|
167
|
-
|
168
|
-
|
169
|
-
|
170
|
-
|
171
|
-
|
172
|
-
cat('\n P-value: ', signif(p.val, 4), sep='');
|
173
|
-
}
|
174
|
-
cat(' ', ifelse(p.val.lim<=0.01, "**", ifelse(p.val.lim<=0.05, "*", "")),
|
232
|
+
(object,
|
233
|
+
...
|
234
|
+
){
|
235
|
+
cat('===[ enve.TRIBStest ]---------------------\n');
|
236
|
+
cat('Alternative hypothesis:\n');
|
237
|
+
cat(' The distances in the selection are\n');
|
238
|
+
if(attr(object, 'pval.gt') > attr(object, 'pval.lt')){
|
239
|
+
cat(' smaller than in the entire dataset\n (overclustering)\n');
|
240
|
+
}else{
|
241
|
+
cat(' larger than in the entire dataset\n (overdispersion)\n');
|
242
|
+
}
|
243
|
+
p.val <- min(attr(object, 'pval.gt'), attr(object, 'pval.lt'));
|
244
|
+
if(p.val==0){
|
245
|
+
diff.dist <- attr(object, 'diff.dist');
|
246
|
+
p.val.lim <- min(diff.dist[diff.dist>0]);
|
247
|
+
cat('\n P-value <= ', signif(p.val.lim, 4), sep='');
|
248
|
+
}else{
|
249
|
+
p.val.lim <- p.val;
|
250
|
+
cat('\n P-value: ', signif(p.val, 4), sep='');
|
251
|
+
}
|
252
|
+
cat(' ', ifelse(p.val.lim<=0.01, "**", ifelse(p.val.lim<=0.05, "*", "")),
|
175
253
|
'\n', sep='');
|
176
|
-
|
177
|
-
|
178
|
-
|
254
|
+
cat('------------------------------------------\n');
|
255
|
+
cat('call:',as.character(attr(object,'call')),'\n');
|
256
|
+
cat('------------------------------------------\n');
|
179
257
|
}
|
180
258
|
|
259
|
+
#' Enveomics: TRIBS Plot Test
|
260
|
+
#'
|
261
|
+
#' Plots an \code{\link{enve.TRIBStest}} object.
|
262
|
+
#'
|
263
|
+
#' @param x
|
264
|
+
#' \code{\link{enve.TRIBStest}} object to plot.
|
265
|
+
#' @param type
|
266
|
+
#' What to plot. \code{overlap} generates a plot of the two contrasting empirical
|
267
|
+
#' PDFs (to compare against each other), \code{difference} produces a plot of the
|
268
|
+
#' differences between the empirical PDFs (to compare against zero).
|
269
|
+
#' @param col
|
270
|
+
#' Main color of the plot if type=\code{difference}.
|
271
|
+
#' @param col1
|
272
|
+
#' First color of the plot if type=\code{overlap}.
|
273
|
+
#' @param col2
|
274
|
+
#' Second color of the plot if type=\code{overlap}.
|
275
|
+
#' @param ylab
|
276
|
+
#' Y-axis label.
|
277
|
+
#' @param xlim
|
278
|
+
#' X-axis limits.
|
279
|
+
#' @param ylim
|
280
|
+
#' Y-axis limits.
|
281
|
+
#' @param ...
|
282
|
+
#' Any other graphical arguments.
|
283
|
+
#'
|
284
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
285
|
+
#'
|
286
|
+
#' @method plot enve.TRIBStest
|
287
|
+
#' @export
|
288
|
+
|
181
289
|
plot.enve.TRIBStest <- function
|
182
|
-
|
183
|
-
|
184
|
-
|
185
|
-
|
186
|
-
|
187
|
-
|
188
|
-
|
189
|
-
|
190
|
-
|
191
|
-
|
192
|
-
|
193
|
-
|
194
|
-
|
195
|
-
|
196
|
-
|
197
|
-
|
198
|
-
|
199
|
-
|
200
|
-
|
201
|
-
|
202
|
-
|
203
|
-
|
204
|
-
|
205
|
-
|
206
|
-
|
207
|
-
|
208
|
-
|
209
|
-
|
210
|
-
|
211
|
-
|
212
|
-
polygon(attr(x, 'dist.mids')[c(1, 1:bins, bins)],
|
213
|
-
c(0,attr(x, 'sel.dist'),0), col=col2,
|
214
|
-
border=do.call(rgb, as.list(c(col2rgb(col2)/256, 0.5))));
|
215
|
-
}else{
|
216
|
-
plot.opts <- list(xlim=range(attr(x, 'diff.mids')),
|
217
|
-
ylim=c(0,max(attr(x, 'diff.dist'))), ylab=ylab, ..., t='n', x=1);
|
218
|
-
do.call(plot, plot.opts);
|
219
|
-
bins <- length(attr(x, 'diff.mids'));
|
220
|
-
polygon(attr(x, 'diff.mids')[c(1, 1:bins, bins)],
|
221
|
-
c(0,attr(x, 'diff.dist'),0), col=col,
|
222
|
-
border=do.call(rgb, as.list(c(col2rgb(col)/256, 0.5))));
|
223
|
-
}
|
290
|
+
(x,
|
291
|
+
type=c('overlap', 'difference'),
|
292
|
+
col='#00000044',
|
293
|
+
col1=col,
|
294
|
+
col2='#44001144',
|
295
|
+
ylab='Probability',
|
296
|
+
xlim=range(attr(x, 'dist.mids')),
|
297
|
+
ylim=c(0,max(c(attr(x, 'all.dist'), attr(x, 'sel.dist')))),
|
298
|
+
...
|
299
|
+
){
|
300
|
+
type <- match.arg(type);
|
301
|
+
if(type=='overlap'){
|
302
|
+
plot.opts <- list(xlim=xlim, ylim=ylim, ylab=ylab, ..., t='n', x=1);
|
303
|
+
do.call(plot, plot.opts);
|
304
|
+
bins <- length(attr(x, 'dist.mids'))
|
305
|
+
polygon(attr(x, 'dist.mids')[c(1, 1:bins, bins)],
|
306
|
+
c(0,attr(x, 'all.dist'),0), col=col1,
|
307
|
+
border=do.call(rgb, as.list(c(col2rgb(col1)/256, 0.5))));
|
308
|
+
polygon(attr(x, 'dist.mids')[c(1, 1:bins, bins)],
|
309
|
+
c(0,attr(x, 'sel.dist'),0), col=col2,
|
310
|
+
border=do.call(rgb, as.list(c(col2rgb(col2)/256, 0.5))));
|
311
|
+
}else{
|
312
|
+
plot.opts <- list(xlim=range(attr(x, 'diff.mids')),
|
313
|
+
ylim=c(0,max(attr(x, 'diff.dist'))), ylab=ylab, ..., t='n', x=1);
|
314
|
+
do.call(plot, plot.opts);
|
315
|
+
bins <- length(attr(x, 'diff.mids'));
|
316
|
+
polygon(attr(x, 'diff.mids')[c(1, 1:bins, bins)],
|
317
|
+
c(0,attr(x, 'diff.dist'),0), col=col,
|
318
|
+
border=do.call(rgb, as.list(c(col2rgb(col)/256, 0.5))));
|
319
|
+
}
|
224
320
|
}
|
225
321
|
|
322
|
+
#' Enveomics: TRIBS Merge
|
323
|
+
#'
|
324
|
+
#' Merges two \code{\link{enve.TRIBS}} objects generated from the same objects at
|
325
|
+
#' different subsampling levels.
|
326
|
+
#'
|
327
|
+
#' @param x
|
328
|
+
#' First \code{\link{enve.TRIBS}} object.
|
329
|
+
#' @param y
|
330
|
+
#' Second \code{\link{enve.TRIBS}} object.
|
331
|
+
#'
|
332
|
+
#' @return Returns an \code{\link{enve.TRIBS}} object.
|
333
|
+
#'
|
334
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
335
|
+
#'
|
336
|
+
#' @export
|
337
|
+
|
226
338
|
enve.TRIBS.merge <- function
|
227
|
-
|
228
|
-
|
229
|
-
|
230
|
-
|
231
|
-
|
232
|
-
|
233
|
-
|
234
|
-
|
235
|
-
|
236
|
-
|
237
|
-
|
238
|
-
|
239
|
-
|
240
|
-
|
241
|
-
|
242
|
-
|
243
|
-
|
244
|
-
|
245
|
-
|
246
|
-
|
247
|
-
|
248
|
-
|
249
|
-
|
250
|
-
|
251
|
-
|
252
|
-
|
253
|
-
|
254
|
-
|
255
|
-
distances=d, spaceSize=attr(x,'spaceSize'),
|
256
|
-
selSize=attr(x,'selSize'), dimensions=attr(x,'dimensions'),
|
257
|
-
subsamples=c(a,b)[o], call=match.call());
|
258
|
-
return(z) ;
|
259
|
-
### Returns an `enve.TRIBS` object.
|
339
|
+
(x,
|
340
|
+
y
|
341
|
+
){
|
342
|
+
# Check consistency
|
343
|
+
if(attr(x,'distance') != attr(y,'distance'))
|
344
|
+
stop('Total distances in objects are different.');
|
345
|
+
if(any(attr(x,'points') != attr(y,'points')))
|
346
|
+
stop('Points in objects are different.');
|
347
|
+
if(attr(x,'spaceSize') != attr(y,'spaceSize'))
|
348
|
+
stop('Space size in objects are different.');
|
349
|
+
if(attr(x,'selSize') != attr(y,'selSize'))
|
350
|
+
stop('Selection size in objects are different.');
|
351
|
+
if(attr(x,'dimensions') != attr(y,'dimensions'))
|
352
|
+
stop('Dimensions in objects are different.');
|
353
|
+
if(nrow(attr(x,'distances')) != nrow(attr(y,'distances')))
|
354
|
+
stop('Replicates in objects are different.');
|
355
|
+
# Merge
|
356
|
+
a <- attr(x,'subsamples');
|
357
|
+
b <- attr(y,'subsamples');
|
358
|
+
o <- order(c(a,b));
|
359
|
+
o <- o[!duplicated(c(a,b)[o])] ;
|
360
|
+
d <- cbind(attr(x,'distances'), attr(y,'distances'))[, o] ;
|
361
|
+
z <- new('enve.TRIBS',
|
362
|
+
distance=attr(x,'distance'), points=attr(x,'points'),
|
363
|
+
distances=d, spaceSize=attr(x,'spaceSize'),
|
364
|
+
selSize=attr(x,'selSize'), dimensions=attr(x,'dimensions'),
|
365
|
+
subsamples=c(a,b)[o], call=match.call());
|
366
|
+
return(z) ;
|
260
367
|
}
|
261
368
|
|
262
369
|
#==============> Define core functions
|
370
|
+
|
371
|
+
#' Enveomics: TRIBS Test
|
372
|
+
#'
|
373
|
+
#' Estimates the empirical difference between all the distances in a set of
|
374
|
+
#' objects and a subset, together with its statistical significance.
|
375
|
+
#'
|
376
|
+
#' @param dist
|
377
|
+
#' Distances as \code{dist} object.
|
378
|
+
#' @param selection
|
379
|
+
#' Selection defining the subset.
|
380
|
+
#' @param bins
|
381
|
+
#' Number of bins to evaluate in the range of distances.
|
382
|
+
#' @param ...
|
383
|
+
#' Any other parameters supported by \code{\link{enve.tribs}},
|
384
|
+
#' except \code{subsamples}.
|
385
|
+
#'
|
386
|
+
#' @return Returns an \code{\link{enve.TRIBStest}} object.
|
387
|
+
#'
|
388
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
389
|
+
#'
|
390
|
+
#' @export
|
391
|
+
|
263
392
|
enve.tribs.test <- function
|
264
|
-
|
265
|
-
|
266
|
-
|
267
|
-
|
268
|
-
|
269
|
-
|
270
|
-
|
271
|
-
|
272
|
-
|
273
|
-
|
274
|
-
|
275
|
-
|
276
|
-
|
277
|
-
|
278
|
-
|
279
|
-
|
280
|
-
|
281
|
-
|
282
|
-
|
283
|
-
|
284
|
-
|
285
|
-
|
286
|
-
|
287
|
-
|
288
|
-
|
289
|
-
|
290
|
-
zz.f <- 0;
|
291
|
-
zp.f[z] <- 0;
|
292
|
-
for(k in 1:length(a.f$mids)){
|
293
|
-
if(z < k){
|
294
|
-
zp.f[z] <- zp.f[z] + p.x[k]*p.y[k-z];
|
295
|
-
zn.f[z] <- zn.f[z] + p.x[k-z]*p.y[k];
|
296
|
-
}
|
297
|
-
zz.f <- zz.f + p.x[k]*p.y[k];
|
393
|
+
(dist,
|
394
|
+
selection,
|
395
|
+
bins=50,
|
396
|
+
...
|
397
|
+
){
|
398
|
+
s.tribs <- enve.tribs(dist, selection, subsamples=c(0,1), ...);
|
399
|
+
a.tribs <- enve.tribs(dist,
|
400
|
+
subsamples=c(0,attr(s.tribs, 'selSize')/attr(s.tribs, 'spaceSize')), ...);
|
401
|
+
s.dist <- attr(s.tribs, 'distances')[, 2];
|
402
|
+
a.dist <- attr(a.tribs, 'distances')[, 2];
|
403
|
+
range <- range(c(s.dist, a.dist));
|
404
|
+
a.f <- hist(a.dist, breaks=seq(range[1], range[2], length.out=bins),
|
405
|
+
plot=FALSE);
|
406
|
+
s.f <- hist(s.dist, breaks=seq(range[1], range[2], length.out=bins),
|
407
|
+
plot=FALSE);
|
408
|
+
zp.f <- c(); zz.f <- 0; zn.f <- c();
|
409
|
+
p.x <- a.f$counts/sum(a.f$counts);
|
410
|
+
p.y <- s.f$counts/sum(s.f$counts);
|
411
|
+
for(z in 1:length(a.f$mids)){
|
412
|
+
zn.f[z] <- 0;
|
413
|
+
zz.f <- 0;
|
414
|
+
zp.f[z] <- 0;
|
415
|
+
for(k in 1:length(a.f$mids)){
|
416
|
+
if(z < k){
|
417
|
+
zp.f[z] <- zp.f[z] + p.x[k]*p.y[k-z];
|
418
|
+
zn.f[z] <- zn.f[z] + p.x[k-z]*p.y[k];
|
298
419
|
}
|
299
|
-
|
300
|
-
|
301
|
-
|
302
|
-
|
303
|
-
|
304
|
-
|
305
|
-
|
306
|
-
|
307
|
-
|
420
|
+
zz.f <- zz.f + p.x[k]*p.y[k];
|
421
|
+
}
|
422
|
+
}
|
423
|
+
return(new('enve.TRIBStest',
|
424
|
+
pval.gt=sum(c(zz.f, zp.f)), pval.lt=sum(c(zz.f, zn.f)),
|
425
|
+
all.dist=p.x, sel.dist=p.y, diff.dist=c(rev(zn.f), zz.f, zp.f),
|
426
|
+
dist.mids=a.f$mids,
|
427
|
+
diff.mids=seq(diff(range(a.f$mids)), -diff(range(a.f$mids)),
|
428
|
+
length.out=1+2*length(a.f$mids)),
|
429
|
+
call=match.call()));
|
308
430
|
}
|
309
431
|
|
432
|
+
#' Enveomics: TRIBS
|
433
|
+
#'
|
434
|
+
#' Subsample any objects in "distance space" to reduce the effect of
|
435
|
+
#' sample-clustering. This function was originally designed to subsample
|
436
|
+
#' genomes in "phylogenetic distance space", a clear case of strong
|
437
|
+
#' clustering bias in sampling, by Luis M. Rodriguez-R and Michael R
|
438
|
+
#' Weigand.
|
439
|
+
#'
|
440
|
+
#' @param dist
|
441
|
+
#' Distances as a \code{dist} object.
|
442
|
+
#' @param selection
|
443
|
+
#' Objects to include in the subsample. By default, all objects are
|
444
|
+
#' selected.
|
445
|
+
#' @param replicates
|
446
|
+
#' Number of replications per point.
|
447
|
+
#' @param summary.fx
|
448
|
+
#' Function to summarize the distance distributions in a given replicate. By
|
449
|
+
#' default, the median distance is estimated.
|
450
|
+
#' @param dist.method
|
451
|
+
#' Distance method between random points and samples in the transformed
|
452
|
+
#' space. See \code{dist}.
|
453
|
+
#' @param subsamples
|
454
|
+
#' Subsampling fractions.
|
455
|
+
#' @param dimensions
|
456
|
+
#' Dimensions to use in the NMDS. By default, 5\% of the selection length.
|
457
|
+
#' @param metaMDS.opts
|
458
|
+
#' Any additional options to pass to metaMDS, as \code{list}.
|
459
|
+
#' @param threads
|
460
|
+
#' Number of threads to use.
|
461
|
+
#' @param verbosity
|
462
|
+
#' Verbosity. Use 0 to run quietly, increase for additional information.
|
463
|
+
#' @param points
|
464
|
+
#' Optional. If passed, the MDS step is skipped and this object is used
|
465
|
+
#' instead. It can be the \code{$points} slot of class \code{metaMDS}
|
466
|
+
#' (from \code{vegan}).
|
467
|
+
#' It must be a matrix or matrix-coercible object, with samples as rows and
|
468
|
+
#' dimensions as columns.
|
469
|
+
#' @param pre.tribs
|
470
|
+
#' Optional. If passed, the points are recovered from this object (except if
|
471
|
+
#' \code{points} is also passed. This should be an \code{\link{enve.TRIBS}} object
|
472
|
+
#' estimated on the same objects (the selection is unimportant).
|
473
|
+
#'
|
474
|
+
#' @return Returns an \code{\link{enve.TRIBS}} object.
|
475
|
+
#'
|
476
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
477
|
+
#'
|
478
|
+
#' @export
|
479
|
+
|
310
480
|
enve.tribs <- function
|
311
|
-
|
312
|
-
|
313
|
-
|
314
|
-
|
315
|
-
|
316
|
-
|
317
|
-
|
318
|
-
|
319
|
-
|
320
|
-
|
321
|
-
|
322
|
-
|
323
|
-
|
324
|
-
|
325
|
-
|
326
|
-
|
327
|
-
|
328
|
-
|
329
|
-
|
330
|
-
|
331
|
-
|
332
|
-
|
333
|
-
|
334
|
-
|
335
|
-
|
336
|
-
|
337
|
-
|
338
|
-
|
339
|
-
points,
|
340
|
-
### Optional. If passed, the MDS step is skipped and this object is used
|
341
|
-
### instead. It can be the `$points` slot of class `metaMDS` (from `vegan`).
|
342
|
-
### It must be a matrix or matrix-coercible object, with samples as rows and
|
343
|
-
### dimensions as columns.
|
344
|
-
pre.tribs
|
345
|
-
### Optional. If passed, the points are recovered from this object (except if
|
346
|
-
### `points` is also passed. This should be an `enve.TRIBS` object estimated
|
347
|
-
### on the same objects (the selection is unimportant).
|
348
|
-
){
|
349
|
-
if(!is(dist, 'dist'))
|
350
|
-
stop('`dist` parameter must be a `dist` object.');
|
351
|
-
# 1. NMDS
|
352
|
-
if(missing(points)){
|
353
|
-
if(missing(pre.tribs)){
|
354
|
-
if(verbosity > 0)
|
355
|
-
cat('===[ Estimating NMDS ]\n');
|
356
|
-
if(!suppressPackageStartupMessages(
|
357
|
-
requireNamespace("vegan", quietly=TRUE)))
|
358
|
-
stop('Unavailable required package: `vegan`.');
|
359
|
-
mds.args <- c(metaMDS.opts, list(comm=dist, k=dimensions,
|
360
|
-
trace=verbosity));
|
361
|
-
points <- do.call(vegan::metaMDS, mds.args)$points;
|
362
|
-
}else{
|
363
|
-
points <- attr(pre.tribs, 'points');
|
364
|
-
dimensions <- ncol(points);
|
365
|
-
}
|
366
|
-
}else{
|
367
|
-
points <- as.matrix(points);
|
481
|
+
(dist,
|
482
|
+
selection=labels(dist),
|
483
|
+
replicates=1000,
|
484
|
+
summary.fx=median,
|
485
|
+
dist.method='euclidean',
|
486
|
+
subsamples=seq(0,1,by=0.01),
|
487
|
+
dimensions=ceiling(length(selection)*0.05),
|
488
|
+
metaMDS.opts=list(),
|
489
|
+
threads=2,
|
490
|
+
verbosity=1,
|
491
|
+
points,
|
492
|
+
pre.tribs
|
493
|
+
){
|
494
|
+
if(!is(dist, 'dist'))
|
495
|
+
stop('`dist` parameter must be a `dist` object.');
|
496
|
+
# 1. NMDS
|
497
|
+
if(missing(points)){
|
498
|
+
if(missing(pre.tribs)){
|
499
|
+
if(verbosity > 0)
|
500
|
+
cat('===[ Estimating NMDS ]\n');
|
501
|
+
if(!suppressPackageStartupMessages(
|
502
|
+
requireNamespace("vegan", quietly=TRUE)))
|
503
|
+
stop('Unavailable required package: `vegan`.');
|
504
|
+
mds.args <- c(metaMDS.opts, list(comm=dist, k=dimensions,
|
505
|
+
trace=verbosity));
|
506
|
+
points <- do.call(vegan::metaMDS, mds.args)$points;
|
507
|
+
}else{
|
508
|
+
points <- attr(pre.tribs, 'points');
|
368
509
|
dimensions <- ncol(points);
|
369
|
-
|
370
|
-
|
371
|
-
|
372
|
-
|
373
|
-
|
374
|
-
|
375
|
-
|
376
|
-
|
377
|
-
|
378
|
-
|
379
|
-
|
380
|
-
|
381
|
-
|
382
|
-
|
383
|
-
|
384
|
-
|
385
|
-
|
386
|
-
|
387
|
-
|
388
|
-
|
389
|
-
|
390
|
-
|
391
|
-
|
392
|
-
|
393
|
-
|
394
|
-
|
395
|
-
|
396
|
-
|
397
|
-
|
398
|
-
|
510
|
+
}
|
511
|
+
}else{
|
512
|
+
points <- as.matrix(points);
|
513
|
+
dimensions <- ncol(points);
|
514
|
+
}
|
515
|
+
# 2. Pad ranges
|
516
|
+
if(verbosity > 0) cat('===[ Padding ranges ]\n');
|
517
|
+
dots <- matrix(NA, nrow=nrow(points), ncol=dimensions,
|
518
|
+
dimnames=list(rownames(points), 1:dimensions));
|
519
|
+
selection <- selection[!is.na(match(selection, rownames(dots)))];
|
520
|
+
for(dim in 1:dimensions){
|
521
|
+
dimRange <- range(points[,dim]) +
|
522
|
+
c(-1,1)*diff(range(points[,1]))/length(selection);
|
523
|
+
dots[, dim] <- (points[,dim]-dimRange[1])/diff(dimRange);
|
524
|
+
}
|
525
|
+
# 3. Select points and summarize distances
|
526
|
+
if(verbosity > 0) cat('===[ Sub-sampling ]\n');
|
527
|
+
distances <- matrix(NA, nrow=replicates, ncol=length(subsamples),
|
528
|
+
dimnames=list(1:replicates, as.character(subsamples)));
|
529
|
+
cl <- makeCluster(threads);
|
530
|
+
for(frx in subsamples){
|
531
|
+
if(verbosity > 1) cat('Sub-sampling at ',(frx*100),'%\n',sep='');
|
532
|
+
distances[, as.character(frx)] = parSapply(cl, 1:replicates, enve.__tribs,
|
533
|
+
frx, match(selection, rownames(dots)), dimensions, dots, dist.method,
|
534
|
+
summary.fx, dist);
|
535
|
+
}
|
536
|
+
stopCluster(cl);
|
537
|
+
# 4. Build object and return
|
538
|
+
return(new('enve.TRIBS',
|
539
|
+
distance=do.call(summary.fx, list(as.matrix(dist)[selection, selection])),
|
540
|
+
points=points, distances=distances, spaceSize=nrow(points),
|
541
|
+
selSize=length(selection), dimensions=dimensions, subsamples=subsamples,
|
542
|
+
call=match.call()));
|
399
543
|
}
|
400
544
|
|
545
|
+
#' Enveomics: TRIBS - Internal Ancillary Function
|
546
|
+
#'
|
547
|
+
#' Internal ancillary function (see \code{\link{enve.tribs}}).
|
548
|
+
#'
|
549
|
+
#' @param rep Replicates
|
550
|
+
#' @param frx Fraction
|
551
|
+
#' @param selection Selection
|
552
|
+
#' @param dimensions Dimensions
|
553
|
+
#' @param dots Sampling points
|
554
|
+
#' @param dist.method Distance method
|
555
|
+
#' @param summary.fx Summary function
|
556
|
+
#' @param dist Distance
|
557
|
+
#'
|
558
|
+
#' @author Luis M. Rodriguez-R [aut, cre]
|
559
|
+
#'
|
560
|
+
#' @export
|
561
|
+
|
401
562
|
enve.__tribs <- function
|
402
|
-
|
403
|
-
|
404
|
-
|
405
|
-
|
406
|
-
|
407
|
-
|
408
|
-
|
409
|
-
|
410
|
-
|
411
|
-
|
412
|
-
|
413
|
-
|
414
|
-
|
415
|
-
closest.dist <- dot.dist;
|
416
|
-
}
|
563
|
+
(rep, frx, selection, dimensions, dots, dist.method, summary.fx, dist){
|
564
|
+
sample <- c();
|
565
|
+
if(frx==0) return(0);
|
566
|
+
for(point in 1:round(frx*length(selection))){
|
567
|
+
rand.point <- runif(dimensions);
|
568
|
+
closest.dot <- '';
|
569
|
+
closest.dist <- Inf;
|
570
|
+
for(dot in selection){
|
571
|
+
dot.dist <- as.numeric(dist(matrix(c(rand.point, dots[dot,]), nrow=2,
|
572
|
+
byrow=TRUE), method=dist.method));
|
573
|
+
if(dot.dist < closest.dist){
|
574
|
+
closest.dot <- dot;
|
575
|
+
closest.dist <- dot.dist;
|
417
576
|
}
|
418
|
-
|
419
|
-
|
420
|
-
|
577
|
+
}
|
578
|
+
sample <- c(sample, closest.dot);
|
579
|
+
}
|
580
|
+
return( do.call(summary.fx, list(as.matrix(dist)[sample, sample])) );
|
421
581
|
}
|
422
582
|
|
423
583
|
|