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Amine GHOZLANE
shaman
Commits
978f4414
Commit
978f4414
authored
Feb 10, 2017
by
Amine GHOZLANE
Browse files
Add more distance
parent
2b5bd3f5
Changes
2
Hide whitespace changes
Inline
Side-by-side
Rfunctions/DiagPlot.R
View file @
978f4414
...
...
@@ -412,35 +412,26 @@ PCoAPlot_meta <-function (input, dds, group_init, CT,tree,col = c("SpringGreen",
# print(head(counts.norm))
## Get the distance
if
(
input
$
DistClust
==
"sere"
)
dist.counts.norm
=
as.dist
(
SEREcoef
(
counts.norm
))
else
if
(
input
$
DistClust
==
"jsd"
){
#dist_jsd = JSD(sweep(counts.norm,2,colSums(counts.norm)))
dist_jsd
=
JSD
(
t
(
sweep
(
counts.norm
,
2
,
colSums
(
counts.norm
),
`/`
)))
dist_jsd
[
is.na
(
dist_jsd
)]
=
0
dist.counts.norm
=
as.dist
(
dist_jsd
)
}
else
if
(
input
$
DistClust
==
"kl"
){
dist_kl
=
KL
(
t
(
sweep
(
counts.norm
,
2
,
colSums
(
counts.norm
),
`/`
)))
dist_kl
[
is.na
(
dist_kl
)]
=
0
dist.counts.norm
=
as.dist
(
dist_kl
)
}
else
if
(
input
$
DistClust
==
"Unifrac"
)
{
else
if
(
input
$
DistClust
==
"Unifrac"
){
tmp
=
UniFracDist
(
CT
,
tree
)
if
(
is.null
(
tree
)
||
is.null
(
tmp
))
dist.counts.norm
=
NULL
if
(
!
is.null
(
tree
))
{
dist.counts.norm
=
switch
(
input
$
DistClustUnifrac
,
"WU"
=
as.dist
(
tmp
[,
,
"d_1"
]),
"UWU"
=
as.dist
(
tmp
[,
,
"d_UW"
]),
"VAWU"
=
as.dist
(
tmp
[,
,
"d_VAW"
])
)
"WU"
=
as.dist
(
tmp
[,
,
"d_1"
]),
"UWU"
=
as.dist
(
tmp
[,
,
"d_UW"
]),
"VAWU"
=
as.dist
(
tmp
[,
,
"d_VAW"
])
)
}
}
else
{
dist.counts.norm
=
vegdist
(
t
(
counts.norm
),
method
=
input
$
DistClust
)
else
if
(
input
$
DistClust
%in%
getDistMethods
()){
dist
=
as.dist
(
distance
(
t
(
sweep
(
counts.norm
,
2
,
colSums
(
counts.norm
),
`/`
)),
method
=
input
$
DistClust
))
dist
[
is.na
(
dist
)]
=
0.0
dist.counts.norm
=
dist
}
else
dist.counts.norm
=
vegdist
(
t
(
counts.norm
),
method
=
input
$
DistClust
)
#"additive_symm"
if
(
!
is.null
(
dist.counts.norm
))
{
## Do PCoA
...
...
@@ -486,8 +477,8 @@ PCoAPlot_meta <-function (input, dds, group_init, CT,tree,col = c("SpringGreen",
title
(
main
=
'Principal Coordinates Analysis '
,
cex.main
=
1.5
)
## Add a subtitle
par
(
font.main
=
3
)
if
(
input
$
DistClust
!=
"Unifrac"
)
title
(
main
=
paste
(
"\n"
,
"\n"
,
input
$
DistClust
,
"distance"
,
sep
=
" "
),
cex.main
=
1
)
if
(
input
$
DistClust
==
"Unifrac"
)
title
(
main
=
paste
(
"\n"
,
"\n"
,
input
$
DistClustUnifrac
,
"distance"
,
sep
=
" "
),
cex.main
=
1
)
else
title
(
main
=
paste
(
"\n"
,
"\n"
,
input
$
DistClust
,
"distance"
,
sep
=
" "
),
cex.main
=
1
)
# Set different shapes
if
(
input
$
labelPCOA
==
"Group"
){
...
...
@@ -649,7 +640,7 @@ Get_pcoa_table <-function (input, dds, group_init,CT,tree)
time_set
=
0
# Set of shape
shape
=
c
(
19
,
17
,
15
,
18
)
## Var of interest
VarInt
=
input
$
VarInt
...
...
@@ -686,16 +677,6 @@ Get_pcoa_table <-function (input, dds, group_init,CT,tree)
## Get the distance
if
(
input
$
DistClust
==
"sere"
)
dist.counts.norm
=
as.dist
(
SEREcoef
(
counts.norm
))
else
if
(
input
$
DistClust
==
"jsd"
){
dist_jsd
=
JSD
(
t
(
sweep
(
counts.norm
,
2
,
colSums
(
counts.norm
),
`/`
)))
dist_jsd
[
is.na
(
dist_jsd
)]
=
0.0
dist.counts.norm
=
as.dist
(
dist_jsd
)
}
else
if
(
input
$
DistClust
==
"kl"
){
dist_kl
=
KL
(
t
(
sweep
(
counts.norm
,
2
,
colSums
(
counts.norm
),
`/`
)))
dist_kl
[
is.na
(
dist_kl
)]
=
0.0
dist.counts.norm
=
as.dist
(
dist_kl
)
}
else
if
(
input
$
DistClust
==
"Unifrac"
)
{
tmp
=
UniFracDist
(
CT
,
tree
)
if
(
is.null
(
tree
)
||
is.null
(
tmp
))
dist.counts.norm
=
NULL
...
...
@@ -706,6 +687,11 @@ Get_pcoa_table <-function (input, dds, group_init,CT,tree)
)
}
}
else
if
(
input
$
DistClust
%in%
getDistMethods
()){
dist
=
as.dist
(
distance
(
t
(
sweep
(
counts.norm
,
2
,
colSums
(
counts.norm
),
`/`
)),
method
=
input
$
DistClust
))
dist
[
is.na
(
dist
)]
=
0.0
dist.counts.norm
=
dist
}
else
{
dist.counts.norm
=
vegdist
(
t
(
counts.norm
),
method
=
input
$
DistClust
)
}
...
...
server.R
View file @
978f4414
...
...
@@ -1551,16 +1551,19 @@ shinyServer(function(input, output,session) {
ErrorTree
=
dataInputTree
()
$
Error
TaxoSelect
=
input
$
TaxoSelect
res
=
selectInput
(
"DistClust"
,
"Distance"
,
c
(
"altGower"
,
"binomial"
,
"bray"
,
"canberra"
,
"cao"
,
"chao"
,
"euclidean"
,
"gower"
,
"horn"
,
"jaccard"
,
"jsd"
,
"kl"
,
"kulczynski"
,
"mahalanobis"
,
"morisita"
,
"mountford"
,
"raup"
,
"SERE"
=
"sere"
),
selected
=
"bray"
)
dist_phyl
=
getDistMethods
()[
!
getDistMethods
()
%in%
c
(
"additive_symm"
,
"jensen-shannon"
,
"jensen_difference"
,
"minkowski"
,
"topsoe"
)]
res
=
selectInput
(
"DistClust"
,
"Distance"
,
unique
(
sort
(
c
(
"altGower"
,
"binomial"
,
"bray"
,
"canberra"
,
"cao"
,
"chao"
,
"euclidean"
,
"gower"
,
"horn"
,
"jaccard"
,
"kulczynski"
,
"mahalanobis"
,
"morisita"
,
"mountford"
,
"raup"
,
"SERE"
=
"sere"
,
dist_phyl
))),
selected
=
"bray"
)
## Add the unifrac distance
if
(
!
is.null
(
tree
)
&&
!
is.null
(
input
$
fileTree
)
&&
is.null
(
ErrorTree
)
&&
TaxoSelect
==
"OTU/Gene"
)
{
res
=
selectInput
(
"DistClust"
,
"Distance"
,
c
(
"altGower"
,
"binomial"
,
"bray"
,
"canberra"
,
"cao"
,
"chao"
,
"euclidean"
,
"gower"
,
"horn"
,
"jaccard"
,
"jsd"
,
"kl"
,
"kulczynski"
,
"mahalanobis"
,
"morisita"
,
"mountford"
,
"raup"
,
"SERE"
=
"sere"
,
"Unifrac"
),
selected
=
"bray"
)
res
=
selectInput
(
"DistClust"
,
"Distance"
,
unique
(
sort
(
c
(
"altGower"
,
"binomial"
,
"bray"
,
"canberra"
,
"cao"
,
"chao"
,
"euclidean"
,
"gower"
,
"horn"
,
"jaccard"
,
"kulczynski"
,
"mahalanobis"
,
"morisita"
,
"mountford"
,
"raup"
,
"SERE"
=
"sere"
,
"Unifrac"
,
dist_phyl
))
),
selected
=
"bray"
)
}
return
(
res
)
...
...
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