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Miroslav Kratochvil
shinyscreen
Commits
907e4903
Commit
907e4903
authored
5 years ago
by
Jessy Krier
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Shiny minimal implementation works
parent
5f4a2ba2
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DESCRIPTION
+3
-1
3 additions, 1 deletion
DESCRIPTION
NAMESPACE
+1
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NAMESPACE
R/mix.R
+180
-0
180 additions, 0 deletions
R/mix.R
with
184 additions
and
1 deletion
DESCRIPTION
+
3
−
1
View file @
907e4903
...
...
@@ -27,4 +27,6 @@ Imports:
yaml,
mzR,
RColorBrewer,
curl
curl,
shiny,
shinydashboard
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NAMESPACE
+
1
−
0
View file @
907e4903
...
...
@@ -5,3 +5,4 @@ export(mb.prep)
export(presc.do)
export(presc.plot)
export(sw.do)
export(presc.shiny)
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R/mix.R
+
180
−
0
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907e4903
...
...
@@ -514,4 +514,184 @@ mb.p<-function(mb,infodir,fn_stgs,cl=F) {
names
(
x
)
<-
names
(
mb
)
x
}
##' Prescreening using shiny interface.
##'
##' @title Prescreening with Shiny
##' @return Nothing useful.
##' @author Jessy Krier
##' @author Mira Narayanan
presc.shiny
<-
function
(
wd
,
mode
,
pal
=
"Dark2"
,
cex
=
0.75
,
rt_digits
=
2
,
m_digits
=
4
){
modemap
=
list
(
pH
=
"MpHp_mass"
,
mH
=
"MmHm_mass"
,
blahnh4
=
"MpNH4_mass"
,
blahna
=
"MpNa_mass"
)
dfdir
<-
file.path
(
wd
,
"prescreen"
)
wd1
<-
wd
[[
1
]]
df
<-
read.csv
(
file
=
get_cmpd_l_fn
(
wd1
),
stringsAsFactors
=
F
)
osmesi
<-
df
$
SMILES
no_cmpds
<-
length
(
osmesi
)
# reconf(wd1)
masses
<-
lapply
(
osmesi
,
function
(
smile
)
{
#osmesi <- tryCatch(RMassBank::findSmiles(i), error = function(e) NA)
zz
<-
RChemMass
::
getSuspectFormulaMass
(
smile
)
zz
[[
modemap
[[
mode
]]]]
})
#message("Masses:",masses)
# return(osmesi)
## Get the basenames of eic files.
eics
<-
list.files
(
path
=
dfdir
[[
1
]],
patt
=
".*eic.csv"
)
maybekids
<-
sapply
(
strsplit
(
eics
,
split
=
"\\."
),
function
(
x
)
{
paste
(
x
[[
1
]][
1
],
'.kids.csv'
,
sep
=
''
)})
idsliderrange
<-
range
(
df
$
ID
)
ui
<-
shinydashboard
::
dashboardPage
(
shinydashboard
::
dashboardHeader
(
title
=
"Prescreening"
),
shinydashboard
::
dashboardSidebar
(
width
=
350
,
shinydashboard
::
sidebarMenu
(
shinydashboard
::
sidebarSearchForm
(
textId
=
"searchText"
,
buttonId
=
"searchButton"
,
label
=
"Search..."
),
shinydashboard
::
menuItem
(
text
=
"Dashboard"
,
tabName
=
"Dashboard"
,
icon
=
shiny
::
icon
(
"dashboard"
)))),
shinydashboard
::
dashboardBody
(
shiny
::
fluidRow
(
shinydashboard
::
box
(
title
=
"MS Prescreening"
,
width
=
6
,
background
=
"blue"
,
""
),
shinydashboard
::
box
(
title
=
"ID N°"
,
width
=
6
,
background
=
"maroon"
,
""
)
),
shiny
::
fluidRow
(
shinydashboard
::
box
(
title
=
"Plot"
,
width
=
6
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
plotOutput
(
"plot1"
,
width
=
"100%"
,
height
=
"400px"
,
click
=
NULL
,
dblclick
=
NULL
,
hover
=
NULL
,
hoverDelay
=
NULL
,
hoverDelayType
=
NULL
,
brush
=
NULL
,
clickId
=
NULL
,
hoverId
=
NULL
)
),
shinydashboard
::
box
(
title
=
"Compounds"
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
""
,
br
(),
sliderInput
(
"idslider"
,
"Compound number:"
,
idsliderrange
[
1
],
idsliderrange
[
2
],
value
=
1
,
step
=
1
)
)
),
shiny
::
fluidRow
(
shinydashboard
::
box
(
title
=
"Plot x axis range"
,
width
=
6
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
shinyUI
(
pageWithSidebar
(
headerPanel
(
""
),
sidebarPanel
(
numericInput
(
"min_val"
,
"Minimum x Axis Value"
,
1
),
numericInput
(
"max_val"
,
"Maximum x Axis Value"
,
100
),
uiOutput
(
"slider"
)),
mainPanel
()
))
),
shinydashboard
::
box
(
title
=
"Prescreening Results"
,
width
=
6
,
solidHeader
=
TRUE
,
collapsible
=
TRUE
,
checkboxGroupInput
(
"variable"
,
"Checkboxes:"
,
c
(
"MS1"
=
"MS1 present"
,
"MS2"
=
"MS2 present"
,
"Alignment"
=
"Alignment MS1/MS2"
,
"Intensity"
=
"Intensity is good"
,
"Noise"
=
"MS is noisy"
)),
textInput
(
"text"
,
"Comments:"
),
tableOutput
(
"data"
)
)
)
)
)
plotall
<-
function
(
i
)
{
eic
<-
eics
[[
i
]]
maybekid
<-
maybekids
[[
i
]]
fn_ini
<-
lapply
(
wd
,
get_stgs_fn
)
lbls
<-
lapply
(
fn_ini
,
function
(
x
)
{
s
<-
yaml
::
yaml.load_file
(
x
);
s
$
prescreen
$
tag
})
dfs
<-
lapply
(
file.path
(
dfdir
,
eic
),
function
(
fn
)
{
tryCatch
(
read.csv
(
fn
,
stringsAsFactors
=
F
),
error
=
function
(
e
)
{
message
(
paste
(
e
,
"; offending file:"
,
fn
))})
})
dfs
<-
lapply
(
dfs
,
function
(
x
)
data.frame
(
rt
=
x
$
rt
/
60
.
,
intensity
=
x
$
intensity
))
## Find existing children.
maybes
<-
file.path
(
dfdir
,
maybekid
)
indkids
<-
which
(
file.exists
(
maybes
))
kids
<-
maybes
[
indkids
]
dfs_kids
<-
lapply
(
kids
,
read.csv
,
stringsAsFactors
=
F
)
dfs_kids
<-
lapply
(
dfs_kids
,
function
(
x
)
data.frame
(
rt
=
x
$
retentionTime
/
60
.
,
intensity
=
-
x
$
intensity
))
## Find max intensities.
w_max
<-
sapply
(
dfs
,
function
(
x
)
which.max
(
x
$
intensity
))
rt_max
<-
Map
(
function
(
df
,
w
)
df
$
rt
[[
w
]],
dfs
,
w_max
)
i_max
<-
Map
(
function
(
df
,
w
)
df
$
intensity
[[
w
]],
dfs
,
w_max
)
symbs
<-
LETTERS
[
1
:
length
(
w_max
)]
## Find max intensities in children
w_max_kids
<-
sapply
(
dfs_kids
,
function
(
x
)
which.max
(
abs
(
x
$
intensity
)))
rt_max_kids
<-
Map
(
function
(
df
,
w
)
df
$
rt
[[
w
]],
dfs_kids
,
w_max_kids
)
i_max_kids
<-
Map
(
function
(
df
,
w
)
df
$
intensity
[[
w
]],
dfs_kids
,
w_max_kids
)
symbs_kids
<-
letters
[
indkids
]
rt_rng
<-
range
(
sapply
(
dfs
,
function
(
x
)
x
$
rt
))
int_rng
<-
range
(
sapply
(
append
(
dfs_kids
,
dfs
),
function
(
x
)
x
$
intensity
))
cols
<-
RColorBrewer
::
brewer.pal
(
n
=
length
(
dfs
),
name
=
pal
)
lgnd
<-
Map
(
function
(
k
,
v
)
paste
(
k
,
"= "
,
formatC
(
v
,
format
=
"f"
,
digits
=
rt_digits
),
sep
=
''
),
symbs
,
rt_max
)
layout
(
matrix
(
c
(
1
,
2
,
3
,
3
),
2
,
2
,
byrow
=
TRUE
),
widths
=
c
(
7
,
8
),
heights
=
c
(
6
,
6
))
struc_xr
<-
c
(
0
,
100
)
struc_yr
<-
c
(
0
,
100
)
plot
(
1
,
1
,
type
=
"n"
,
xlab
=
""
,
ylab
=
""
,
xlim
=
struc_xr
,
ylim
=
struc_yr
,
xaxt
=
"n"
,
yaxt
=
"n"
)
rendersmiles2
(
osmesi
[
i
],
coords
=
c
(
struc_xr
[
1
],
struc_yr
[
1
],
struc_xr
[
2
],
struc_yr
[
2
]))
col_eng
<-
c
(
0
,
100
)
peak_int
<-
c
(
0
,
100
)
plot
(
1
,
1
,
type
=
"n"
,
xlab
=
""
,
ylab
=
""
,
xlim
=
col_eng
,
ylim
=
peak_int
,
xaxt
=
"n"
,
yaxt
=
"n"
,
axes
=
FALSE
)
linfo
<-
legend
(
"topleft"
,
horiz
=
T
,
legend
=
lbls
,
col
=
cols
,
fill
=
cols
,
bty
=
"n"
,
cex
=
cex
)
legend
(
x
=
linfo
$
rect
$
left
,
y
=
linfo
$
rect
$
top
-0.5
*
linfo
$
rect
$
h
,
horiz
=
T
,
legend
=
lgnd
,
fill
=
cols
,
bty
=
'n'
,
cex
=
cex
)
cols_kids
<-
cols
[
indkids
]
lgnd_kids
<-
Map
(
function
(
k
,
v
)
paste
(
k
,
"= "
,
formatC
(
v
,
digits
=
rt_digits
,
format
=
"f"
),
sep
=
''
),
symbs_kids
,
rt_max_kids
)
if
(
length
(
lgnd_kids
)
>
0
)
legend
(
x
=
linfo
$
rect
$
left
,
y
=
linfo
$
rect
$
top
-1
*
linfo
$
rect
$
h
,
horiz
=
T
,
legend
=
lgnd_kids
,
fill
=
cols
[
indkids
],
bty
=
"n"
,
cex
=
cex
)
plot
(
1
,
1
,
xlab
=
""
,
ylab
=
""
,
xlim
=
rt_rng
,
ylim
=
int_rng
,
type
=
"n"
)
## Plot eic across the directory set.
for
(
n
in
seq
(
length
(
dfs
)))
{
df
<-
dfs
[[
n
]]
col
<-
cols
[[
n
]]
lines
(
df
$
intensity
~
df
$
rt
,
col
=
col
)
}
if
(
length
(
dfs_kids
)
>
0
)
{
for
(
k
in
1
:
length
(
indkids
))
{
lines
(
intensity
~
rt
,
data
=
dfs_kids
[[
k
]],
type
=
"h"
,
col
=
cols_kids
[[
k
]])
}
}
title
(
main
=
paste
(
"ID:"
,
i
,
"Ion m:"
,
formatC
(
masses
[[
i
]],
digits
=
m_digits
,
format
=
"f"
)),
xlab
=
"retention time [min]"
,
ylab
=
"intensity"
)
for
(
k
in
seq
(
length
(
w_max
)))
text
(
rt_max
[[
k
]],
i_max
[[
k
]],
labels
=
symbs
[[
k
]],
pos
=
4
,
offset
=
0.5
*
k
)
if
(
length
(
dfs_kids
)
>
0
)
for
(
k
in
seq
(
length
(
w_max_kids
)))
text
(
rt_max_kids
[[
k
]],
i_max_kids
[[
k
]],
labels
=
symbs_kids
[[
k
]],
pos
=
4
,
offset
=
0.5
*
k
)
axis
(
1
)
axis
(
2
)
## RChemMass::renderSMILES.rcdk(smiles[[i]],coords=c(x1,y1,x2,y2))
gc
()
}
server
<-
function
(
input
,
output
)
{
output
$
plot1
<-
renderPlot
(
{
i
=
input
$
idslider
plotall
(
i
)
}
)
}
shiny
::
shinyApp
(
ui
=
ui
,
server
=
server
)
}
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