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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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umrf
ranomaly
Commits
be723e90
Commit
be723e90
authored
Oct 01, 2021
by
Etienne Rifa
Browse files
Merge branch 'master' into bars_update
parents
68f24906
af195182
Changes
2
Hide whitespace changes
Inline
Side-by-side
R/aggregate_fun.R
View file @
be723e90
...
...
@@ -46,9 +46,9 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
if
(
!
dir.exists
(
output
)){
dir.create
(
output
,
recursive
=
T
)
}
flog.info
(
'Done.'
)
# data.glom <- tax_glom(data, taxrank=rank, h=TRUE)
flog.info
(
'Glom Tax.'
)
data.glom
<-
tax_glom
(
data
,
taxrank
=
rank
)
if
(
comp
==
''
){
fun
<-
paste
(
'combinaisons <- combn(na.omit(unique(sample_data(data)$'
,
column1
,
')),2)'
,
sep
=
''
)
...
...
@@ -176,7 +176,7 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
names
(
TABf
)[
ncol
(
TABf
)]
=
names
(
TF
)[
j
]
}
TABfbak
<-
TABf
TABfbak
0
<-
TABf
# add new columns, sumMethods, DeseqLFC, Mean Relative Abundance (TSS) condition 1 & 2
row.names
(
deseqT
)
=
deseqT
[,
1
]
...
...
@@ -192,7 +192,7 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
# clr = function(x){log(x+1) - rowMeans(log(x+1))}
# otableNORM <- clr(otable)
normf
=
function
(
x
){
x
/
sum
(
x
)
}
data.norm
<-
transform_sample_counts
(
data
,
normf
)
data.norm
<-
transform_sample_counts
(
data
.glom
,
normf
)
otableNORM
<-
otu_table
(
data.norm
)
Gtab
<-
cbind
(
as.data.frame
(
ssample
),
t
(
otableNORM
))
...
...
R/diversity_beta_light.R
View file @
be723e90
...
...
@@ -11,6 +11,7 @@
#' @param output The output file directory.
#' @param tests Whether to compute tests or not (TRUE/FALSE)
#' @param axes Axes to plot (c(1,2))
#' @param ellipse Plot ellipse (TRUE)
#' @param verbose Verbose level. (1: quiet, 2: print infos, 3: print infos + debug)
#'
#' @return Return specific plots and tests in list and output them in the output directory.
...
...
@@ -26,7 +27,7 @@
# Decontam Function
diversity_beta_light
<-
function
(
psobj
,
rank
=
"ASV"
,
col
=
NULL
,
cov
=
NULL
,
dist0
=
"bray"
,
ord0
=
"MDS"
,
output
=
"./plot_div_beta/"
,
axes
=
c
(
1
,
2
),
tests
=
TRUE
,
verbose
=
2
)
{
diversity_beta_light
<-
function
(
psobj
,
rank
=
"ASV"
,
col
=
NULL
,
cov
=
NULL
,
dist0
=
"bray"
,
ord0
=
"MDS"
,
output
=
"./plot_div_beta/"
,
axes
=
c
(
1
,
2
),
tests
=
TRUE
,
verbose
=
2
,
ellipse
=
TRUE
)
{
if
(
verbose
==
3
){
invisible
(
flog.threshold
(
DEBUG
))
...
...
@@ -70,11 +71,32 @@ diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, di
flog.info
(
'Plot ...'
)
resBeta
<-
list
()
if
(
!
is.null
(
cov
)){
sdata
=
sample_data
(
data_rank
)
fun
=
glue
::
glue
(
"sdata${cov1[length(cov1)]}_{col} = factor(paste(sdata${cov1[length(cov1)]}, sdata${col}, sep='_'))"
)
eval
(
parse
(
text
=
fun
))
sample_data
(
data_rank
)
=
sdata
p1
<-
plot_samples
(
data_rank
,
ordinate
(
data_rank
,
ord0
,
dist0
),
color
=
col
,
shape
=
cov1
[
length
(
cov1
)],
axes
=
axes
)
+
theme_bw
()
+
ggtitle
(
glue
::
glue
(
"{ord0} + {dist0}"
))
+
stat_ellipse
()
+
scale_shape_manual
(
values
=
0
:
10
)
theme_bw
()
+
ggtitle
(
glue
::
glue
(
"{ord0} + {dist0}"
))
+
scale_shape_manual
(
values
=
0
:
10
)
if
(
ellipse
){
p1
<-
p1
+
stat_ellipse
()}
p2
<-
plot_samples
(
data_rank
,
ordinate
(
data_rank
,
ord0
,
dist0
),
color
=
glue
::
glue
(
"{cov1[length(cov1)]}_{col}"
),
shape
=
NULL
,
axes
=
axes
)
+
theme_bw
()
+
ggtitle
(
glue
::
glue
(
"{ord0} + {dist0}"
))
+
scale_shape_manual
(
values
=
0
:
10
)
if
(
ellipse
){
p2
<-
p2
+
stat_ellipse
()}
resBeta
$
plot2
<-
p2
+
theme
(
axis.text.x
=
element_text
(
angle
=
45
,
hjust
=
1
),
,
axis.text
=
element_text
(
size
=
18
),
axis.title
=
element_text
(
size
=
16
,
face
=
"bold"
),
strip.text.x
=
element_text
(
size
=
18
,
face
=
"bold"
),
title
=
element_text
(
size
=
16
,
face
=
"bold"
))
ggsave
(
glue
::
glue
(
"{output}/beta_diversity2.eps"
),
plot
=
resBeta
$
plot2
,
height
=
20
,
width
=
30
,
units
=
"cm"
,
dpi
=
500
,
device
=
"eps"
)
}
else
{
p1
<-
plot_samples
(
data_rank
,
ordinate
(
data_rank
,
ord0
,
dist0
),
color
=
col
,
axes
=
axes
)
+
theme_bw
()
+
ggtitle
(
glue
::
glue
(
"{ord0} + {dist0}"
))
+
stat_ellipse
()
theme_bw
()
+
ggtitle
(
glue
::
glue
(
"{ord0} + {dist0}"
))
if
(
ellipse
){
p1
<-
p1
+
stat_ellipse
()}
}
# plot(p1)
flog.info
(
'Plot ok...'
)
...
...
@@ -105,10 +127,9 @@ diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, di
}
#PairwiseAdonis
# resBC2 = pairwise.adonis2(as.formula( paste('BC.dist ~ ', col,sep="") ), data = mdata)
if
(
length
(
col1
)
>
1
){
fact1
<-
apply
(
mdata
[,
c
(
col1
)]
,
1
,
paste
,
collapse
=
"-"
)
resBC2
<-
pairwise.adonis
(
dist1
,
fact1
,
p.adjust.m
=
'fdr'
)
if
(
!
is.null
(
cov
)){
fun
=
glue
::
glue
(
"resBC2 <- pairwise.adonis(dist1, mdata${cov1[length(cov1)]}_{col}, p.adjust.m='fdr')"
)
eval
(
parse
(
text
=
fun
))
}
else
{
resBC2
<-
pairwise.adonis
(
dist1
,
mdata
[,
c
(
col1
)],
p.adjust.m
=
'fdr'
)
}
...
...
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