Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Antonio Politi
NPCMaturation
Commits
a3e6801d
Commit
a3e6801d
authored
Aug 26, 2016
by
Antonio Politi
Browse files
Plotting function R
parent
067d60d4
Changes
7
Hide whitespace changes
Inline
Side-by-side
rcode/distributedDelay_densities.R
0 → 100644
View file @
a3e6801d
# ----
library
(
"ggplot2"
)
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
inData
=
list
()
fname
<-
'delayedMaturation_v0.015_ts10_den.txt'
tmpCsv
=
read.csv
(
fname
,
skip
=
0
,
sep
=
'\t'
)
tmpCsv
[
'dtauM'
]
=
0
tmpCsv
[
'idx'
]
=
6
inData
=
rbind
(
inData
,
tmpCsv
)
delay
=
c
(
5
,
10
,
15
,
20
,
30
)
for
(
idx
in
seq
(
1
,
length
(
delay
),
1
))
{
fname
<-
paste
(
c
(
'delayedMaturationDistrubutedDelay_ts10_v0.015_dtau'
,
as.character
(
delay
[
idx
]),
'_den.txt'
),
collapse
=
''
)
tmpCsv
=
read.csv
(
fname
,
skip
=
0
,
sep
=
'\t'
)
tmpCsv
[
'dtauM'
]
=
delay
[
idx
]
tmpCsv
[
'idx'
]
=
length
(
delay
)
-
idx
inData
=
rbind
(
inData
,
tmpCsv
)
}
# -----
addOpt
<-
function
(
p
)
{
p
<-
p
+
xlab
(
' Time after AO (min)'
)
+
ylab
(
expression
(
paste
(
"Density (pores/"
,
mu
,
m
^
2
,
")"
)))
+
scale_x_continuous
(
expand
=
c
(
0
,
0
),
limits
=
c
(
0
,
120
),
breaks
=
seq
(
0
,
120
,
20
))
+
scale_y_continuous
(
expand
=
c
(
0
,
0
),
limits
=
c
(
0
,
13
),
breaks
=
seq
(
0
,
13
,
4
))
+
theme_classic
(
base_size
=
8
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
return
(
p
)
}
# ----
pint
<-
ggplot
(
data
=
inData
)
+
geom_line
(
data
=
inData
,
aes
(
time
,
inter_i
,
group
=
idx
,
colour
=
-
idx
))
+
geom_line
(
data
=
inData
,
aes
(
time
,
mature_i
,
group
=
idx
,
colour
=
idx
))
#pmat <- ggplot(data = inData) +
# geom_line(aes(time, mature_i, group = N+200, colour = N+200))
pint
<-
addOpt
(
pint
)
+
scale_color_gradient2
(
midpoint
=
0
,
low
=
"red"
,
mid
=
"gray"
,
high
=
"blue"
)
#pint <- addOpt(pint) + scale_color_gradient2(midpoint = 0,space='Lab', low="black", mid = "gray", high="black")
pint
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
)
}
ggsave
(
filename
=
"inner_distributedDelay.pdf"
,
plot
=
pint
,
width
=
71
,
height
=
44
,
units
=
'mm'
)
gp
<-
ggplot_build
(
pint
)
cp
<-
unique
(
gp
$
data
[[
1
]][
"colour"
])
# -----
cols
=
c
(
"#BEBEBE"
,
"#9B9B9B"
,
"#7A7A7A"
,
"#5B5B5B"
,
"#3D3D3D"
,
"#000000"
)
dtauM_distr
=
c
(
0.1
,
5
,
10
,
15
,
20
,
30
)
times
=
seq
(
20
,
60
,
0.1
)
distr
=
list
()
for
(
dtau
in
dtauM_distr
){
distrloc
=
data.frame
(
time
=
seq
(
20
,
60
,
0.1
),
dis
=
0
,
dtauM
=
0
)
distrloc
$
dis
=
1
/
dtau
*
(
distrloc
$
time
>
40
-
dtau
/
2
)
*
(
distrloc
$
time
<
40
+
dtau
/
2
)
distrloc
$
dtauM
=
dtau
distr
=
rbind
(
distr
,
distrloc
)
}
distr
$
dtauM
=
factor
(
distr
$
dtauM
,
c
(
0.1
,
5
,
10
,
15
,
20
,
30
))
pdtauM
<-
ggplot
()
+
geom_line
(
data
=
distr
,
aes
(
x
=
time
,
y
=
dis
,
group
=
dtauM
,
colour
=
dtauM
))
+
theme_classic
(
base_size
=
8
)
+
xlab
(
'Maturtion time (min)'
)
+
scale_colour_manual
(
values
=
cols
[
seq
(
6
,
1
,
-1
)])
+
ylab
(
'Probability'
)
+
coord_cartesian
(
ylim
=
c
(
0
,
0.3
))
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
pdtauM
ggsave
(
filename
=
"distributedDelay_dtauM.pdf"
,
plot
=
pdtauM
,
width
=
72
,
height
=
22
,
units
=
'mm'
)
rcode/distributedDelayvsdelayequation.R
0 → 100644
View file @
a3e6801d
library
(
"ggplot2"
)
# ----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
indatadir
<-
'/Users/toni/Dropbox/NPCMaturation/expdata/emdata'
indir
<-
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
outdir
<-
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
}
else
{
indatadir
<-
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\expdata\\emdata'
indir
<-
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
outdir
<-
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
}
setwd
(
indir
)
inData
=
list
()
fname
<-
'delayedMaturation_v0.015_ts10.txt'
tmpCsv
=
read.csv
(
fname
,
skip
=
6
,
sep
=
'\t'
)
idx
=
which.min
(
tmpCsv
$
norm
)
concatDF
=
tmpCsv
[
idx
,]
concatDF
[
'dtauM'
]
=
0
concatDF
[
'idx'
]
=
0
inData
=
rbind
(
inData
,
concatDF
[,
c
(
'idx'
,
'norm'
,
'tauM'
,
'dtauM'
)])
delay
=
c
(
5
,
10
,
15
,
20
,
30
)
for
(
idx
in
seq
(
1
,
length
(
delay
),
1
))
{
fname
<-
paste
(
c
(
'delayedMaturationDistrubutedDelay_ts10_v0.015_dtau'
,
as.character
(
delay
[
idx
]),
'.txt'
),
collapse
=
''
)
tmpCsv
=
read.csv
(
fname
,
skip
=
6
,
sep
=
'\t'
)
idxC
=
which.min
(
tmpCsv
$
norm
)
concatDF
=
tmpCsv
[
idxC
,]
concatDF
[
'idx'
]
=
idx
concatDF
[
'dtauM'
]
=
concatDF
[
'dtauM'
]
/
2
inData
=
rbind
(
inData
,
concatDF
[,
c
(
'idx'
,
'norm'
,
'tauM'
,
'dtauM'
)])
}
inData
$
dtauM
=
factor
(
inData
$
dtauM
,
levels
=
c
(
0
,
5
,
10
,
15
,
20
,
30
)
/
2
)
inData
$
idx
=
factor
(
inData
$
idx
,
levels
=
c
(
0
,
1
,
2
,
3
,
4
,
5
))
# ----
cols
=
c
(
"#BEBEBE"
,
"#9B9B9B"
,
"#7A7A7A"
,
"#5B5B5B"
,
"#3D3D3D"
,
"#000000"
)
pChi2
<-
ggplot
(
inData
,
aes
(
x
=
dtauM
,
y
=
norm
,
fill
=
idx
))
+
geom_bar
(
stat
=
"identity"
,
position
=
'dodge'
)
+
coord_cartesian
(
ylim
=
c
(
20
,
40
))
+
theme_classic
(
base_size
=
8
)
+
xlab
(
'Half-width distribution (min)'
)
+
ylab
(
'Sum of squared \n residuals'
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_blank
(),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
+
scale_fill_manual
(
values
=
cols
[
seq
(
6
,
1
,
-1
)])
pChi2
setwd
(
outdir
)
ggsave
(
filename
=
"distributedDelay_chi2.pdf"
,
plot
=
pChi2
,
width
=
71
,
height
=
30
,
units
=
'mm'
)
# ----
ptaum
<-
ggplot
(
inData
,
aes
(
x
=
dtauM
,
y
=
tauM
,
fill
=
idx
))
+
geom_bar
(
stat
=
"identity"
,
position
=
'dodge'
)
+
theme_classic
(
base_size
=
8
)
+
xlab
(
'Half-width distribution (min)'
)
+
scale_fill_manual
(
values
=
cols
[
seq
(
6
,
1
,
-1
)])
+
ylab
(
'Avg. Mat. time (min)\n'
)
+
coord_cartesian
(
ylim
=
c
(
0
,
50
),
xlim
=
c
(
0.4
,
6.6
),
expand
=
c
(
0
))
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
ptaum
ggsave
(
filename
=
"distributedDelay_tauM.pdf"
,
plot
=
ptaum
,
width
=
71
,
height
=
35
,
units
=
'mm'
)
#----
rcode/linearChainvsdelayequation.R
0 → 100644
View file @
a3e6801d
library
(
"ggplot2"
)
# ----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/linearChain'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\linearChain'
)
}
inData
=
list
()
for
(
N
in
c
(
5
,
10
,
20
,
40
,
100
))
{
tmpCsv
=
read.csv
(
paste
(
c
(
'linearChainApproximation_N'
,
as.character
(
N
),
'_v0.015.txt'
),
collapse
=
''
)
,
skip
=
6
,
sep
=
'\t'
)
tmpCsv
[
'N'
]
=
N
tmpCsv
[
'model'
]
=
'multi step'
colnames
(
tmpCsv
)[
1
]
<-
'ts'
idx
=
which.min
(
tmpCsv
$
norm
)
concatDF
=
tmpCsv
[
idx
,]
concatDF
[
'tauM'
]
=
(
N
-1
)
/
concatDF
$
k
inData
=
rbind
(
inData
,
concatDF
[,
c
(
'norm'
,
'N'
,
'model'
,
'tauM'
)])
}
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
fname
<-
'delayedMaturation_v0.015_ts10.txt'
tmpCsv
=
read.csv
(
fname
,
skip
=
6
,
sep
=
'\t'
)
colnames
(
tmpCsv
)[
1
]
<-
'ts'
colnames
(
tmpCsv
)[
3
]
<-
'k'
idx
=
which.min
(
tmpCsv
$
norm
)
concatDF
=
tmpCsv
[
idx
,]
concatDF
[
'model'
]
=
'delay'
concatDF
[
'N'
]
=
'delay'
inData
=
rbind
(
inData
,
concatDF
[,
c
(
'norm'
,
'N'
,
'model'
,
'tauM'
)])
inData
$
N
=
factor
(
inData
$
N
,
levels
=
c
(
5
,
10
,
20
,
40
,
100
,
'delay'
))
# ----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
)
}
cols
=
c
(
"#BEBEBE"
,
"#9B9B9B"
,
"#7A7A7A"
,
"#5B5B5B"
,
"#3D3D3D"
,
"#000000"
)
pChi2
<-
ggplot
(
inData
,
aes
(
x
=
N
,
y
=
norm
,
fill
=
N
))
+
geom_bar
(
stat
=
"identity"
,
position
=
'dodge'
)
+
coord_cartesian
(
ylim
=
c
(
20
,
40
))
+
theme_classic
(
base_size
=
8
)
+
xlab
(
''
)
+
ylab
(
'Sum of squared \n residuals'
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_blank
(),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
+
scale_fill_manual
(
values
=
cols
)
pChi2
ggsave
(
filename
=
"linearChain_delay_chi2.pdf"
,
plot
=
pChi2
,
width
=
71
,
height
=
30
,
units
=
'mm'
)
# ----
ptaum
<-
ggplot
(
inData
,
aes
(
x
=
N
,
y
=
tauM
,
fill
=
N
))
+
geom_bar
(
stat
=
"identity"
,
position
=
'dodge'
)
+
theme_classic
(
base_size
=
8
)
+
xlab
(
'Number of steps (N)'
)
+
scale_fill_manual
(
values
=
cols
)
+
ylab
(
'Maturation time (min)\n'
)
+
coord_cartesian
(
ylim
=
c
(
0
,
50
),
xlim
=
c
(
0.4
,
6.6
),
expand
=
c
(
0
))
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
ptaum
ggsave
(
filename
=
"linearChain_delay_tauM.pdf"
,
plot
=
ptaum
,
width
=
71
,
height
=
35
,
units
=
'mm'
)
rcode/linearChainvsdelayequation_densities.R
0 → 100644
View file @
a3e6801d
# ----
library
(
"ggplot2"
)
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/linearChain'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\linearChain'
)
}
inData
=
list
()
Nval
=
c
(
5
,
10
,
20
,
40
,
100
)
for
(
idx
in
c
(
1
,
2
,
3
,
4
,
5
))
{
fname
<-
paste
(
c
(
'linearChainApproximation_N'
,
as.character
(
Nval
[
idx
]),
'_v0.015_den.txt'
),
collapse
=
''
)
tmpCsv
=
read.csv
(
fname
,
skip
=
0
,
sep
=
'\t'
)
tmpCsv
[
'N'
]
=
Nval
[
idx
]
tmpCsv
[
'id'
]
=
idx
-1
inData
=
rbind
(
inData
,
tmpCsv
)
}
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
fname
<-
'delayedMaturation_v0.015_ts10_den.txt'
tmpCsv
=
read.csv
(
fname
,
skip
=
0
,
sep
=
'\t'
)
tmpCsv
[
'N'
]
=
1000
tmpCsv
[
'id'
]
=
5
inData
=
rbind
(
inData
,
tmpCsv
)
addOpt
<-
function
(
p
)
{
p
<-
p
+
xlab
(
' Time after AO (min)'
)
+
ylab
(
expression
(
paste
(
"Density (pores/"
,
mu
,
m
^
2
,
")"
)))
+
scale_x_continuous
(
expand
=
c
(
0
,
0
),
limits
=
c
(
0
,
120
),
breaks
=
seq
(
0
,
120
,
20
))
+
scale_y_continuous
(
expand
=
c
(
0
,
0
),
limits
=
c
(
0
,
13
),
breaks
=
seq
(
0
,
13
,
4
))
+
theme_classic
(
base_size
=
8
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
return
(
p
)
}
# ----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
)
}
pint
<-
ggplot
(
data
=
inData
)
+
geom_line
(
data
=
inData
,
aes
(
time
,
inter_i
,
group
=
id
,
colour
=
-
id
))
+
geom_line
(
data
=
inData
,
aes
(
time
,
mature_i
,
group
=
id
,
colour
=
id
))
#pmat <- ggplot(data = inData) +
# geom_line(aes(time, mature_i, group = N+200, colour = N+200))
pint
<-
addOpt
(
pint
)
+
scale_color_gradient2
(
midpoint
=
0
,
low
=
"red"
,
mid
=
"gray"
,
high
=
"blue"
)
pint
ggsave
(
filename
=
"inner_linearChain_delay.pdf"
,
plot
=
pint
,
width
=
71
,
height
=
44
,
units
=
'mm'
)
gp
<-
ggplot_build
(
pint
)
cp
<-
unique
(
gp
$
data
[[
1
]][
"colour"
])
rcode/prodVariants.R
0 → 100644
View file @
a3e6801d
# ----
library
(
"ggplot2"
)
# ------
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
fnames
=
c
(
'delayedMaturation_v0_ts10.txt'
,
'delayedMaturation_noPrecursor_ts10.txt'
,
'delayedMaturationExponentialV_noPrecursor_ts10_v0.015.txt'
,
'delayedMaturation_v0.015_ts10.txt'
,
'delayedMaturationExponentialV_ts10_v0.015.txt'
)
#vbasal is kept constant
#nrpar = c(6, 5, 6, 6, 8)
nrpar
=
c
(
6
,
5
,
7
,
7
,
8
)
# fnames = c('delayedMaturation_v0_ts10.txt',
# 'delayedMaturation_noPrecursor_ts10.txt',
# 'delayedMaturationExponentialV_noPrecursor_ts10.txt',
# 'delayedMaturationSteadyRho_noPrecursor_ts10.txt',
# 'delayedMaturation_ts10.txt',
# 'delayedMaturationExponentialV_ts10.txt',
# 'delayedMaturationSteadyRho_ts10.txt')
#
#nrpar = c(6, 5, 7, 6, 7, 9, 8)
varNames
=
c
(
'Var 1'
,
'Var 2'
,
'Var 3'
,
'Var 1+2'
,
'Var 1+3'
)
inData
=
list
()
seq_plot
=
c
(
1
,
2
,
3
,
4
,
5
)
for
(
i
in
seq_along
(
fnames
)
)
{
tmpCsv
=
read.csv
(
fnames
[
i
],
skip
=
6
,
sep
=
'\t'
)
tmpCsv
[
'model'
]
=
varNames
[
i
]
tmpCsv
[
'nrpar'
]
=
nrpar
[
i
]
idx
=
which.min
(
tmpCsv
$
norm
)
inData
=
rbind
(
inData
,
tmpCsv
[
idx
,
c
(
'tauM'
,
'norm'
,
'model'
,
'nrpar'
)])
}
inData
$
model
=
factor
(
inData
$
model
,
levels
=
varNames
[
seq_plot
])
#-----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
)
}
pChi2
<-
ggplot
(
inData
,
aes
(
x
=
model
,
y
=
norm
,
fill
=
model
))
+
geom_bar
(
stat
=
"identity"
)
+
coord_cartesian
(
ylim
=
c
(
20
,
55
))
+
theme_classic
(
base_size
=
8
)
+
xlab
(
''
)
+
ylab
(
'Sum of squared \n residuals'
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_blank
(),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
pChi2
gp
<-
ggplot_build
(
pChi2
)
cp
<-
unique
(
gp
$
data
[[
1
]][
"fill"
])
ggsave
(
filename
=
"production_rates_Chi2.pdf"
,
plot
=
pChi2
,
width
=
71
,
height
=
30
,
units
=
'mm'
)
# -----
ptaum
<-
ggplot
(
inData
,
aes
(
x
=
model
,
y
=
tauM
,
fill
=
model
))
+
geom_bar
(
stat
=
"identity"
)
+
coord_cartesian
(
ylim
=
c
(
0
,
50
),
expand
=
c
(
0
),
xlim
=
c
(
0.4
,
5.6
))
+
theme_classic
(
base_size
=
8
)
+
xlab
(
''
)
+
ylab
(
'Maturation time (min)\n'
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
,
angle
=
45
,
vjust
=
0.5
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
ptaum
ggsave
(
filename
=
"production_rates_tauM.pdf"
,
plot
=
ptaum
,
width
=
71
,
height
=
43
,
units
=
'mm'
)
# ----
testPairs
=
rbind
(
c
(
1
,
2
),
c
(
1
,
3
),
c
(
1
,
4
),
c
(
1
,
5
),
c
(
2
,
3
),
c
(
2
,
4
),
c
(
2
,
5
),
c
(
3
,
5
))
for
(
i
in
seq
(
1
,
8
,
1
))
{
print
(
1
-
pchisq
(
abs
(
inData
$
norm
[
testPairs
[
i
,
1
]]
-
inData
$
norm
[
testPairs
[
i
,
2
]]),
abs
(
inData
$
nrpar
[
testPairs
[
i
,
2
]]
-
inData
$
nrpar
[
testPairs
[
i
,
1
]])))
}
#----
#----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
fnames
=
c
(
'delayedMaturation_v0_ts10_prodrate.txt'
,
'delayedMaturation_noPrecursor_ts10_prodrate.txt'
,
'delayedMaturationExponentialV_noPrecursor_ts10_v0.015_prodrate.txt'
,
'delayedMaturation_v0.015_ts10_prodrate.txt'
,
'delayedMaturationExponentialV_ts10_v0.015_prodrate.txt'
)
inData
=
list
()
seq_plot
=
c
(
1
,
4
,
2
,
5
,
3
)
for
(
i
in
seq_along
(
fnames
)
)
{
tmpCsv
=
read.csv
(
fnames
[
i
],
skip
=
0
,
sep
=
'\t'
)
tmpCsv
[
'model'
]
=
varNames
[
i
]
if
(
i
==
2
||
i
==
3
||
i
==
5
)
{
tmpCsv
[
'ProdDensity_inner'
]
=
tmpCsv
[
'ProdDensity_inner'
]
*
0.25
}
inData
=
rbind
(
inData
,
tmpCsv
)
}
inData
$
model
=
factor
(
inData
$
model
,
levels
=
varNames
[
seq_plot
])
p
<-
ggplot
(
inData
,
aes
(
time
,
ProdDensity_inner
,
colour
=
model
))
+
geom_line
(
size
=
1
)
+
theme_classic
(
base_size
=
8
)
+
coord_cartesian
(
ylim
=
c
(
0
,
0.1
),
xlim
=
c
(
0
,
50
))
+
facet_wrap
(
~
model
,
ncol
=
2
)
+
xlab
(
'Time after AO (min)'
)
+
ylab
(
'Production density (pores/um2/min)'
)
+
theme
(
legend.position
=
'none'
,
strip.background
=
element_blank
(),
axis.line.y
=
element_blank
(),
#element_line(color="black", size = 0.5),
axis.line.x
=
element_blank
(),
strip.text.x
=
element_text
(
size
=
8
,
angle
=
0
),
legend.key
=
element_blank
(),
#axis.text.x = element_blank(),
#axis.text.y = element_blank(),
#axis.ticks.x=element_blank(),
#axis.ticks.y=element_blank(),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
+
scale_colour_manual
(
values
=
cp
$
fill
[
seq_plot
])
p
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
)
}
ggsave
(
filename
=
"production_rates.pdf"
,
plot
=
p
,
width
=
100
,
height
=
60
,
units
=
'mm'
)
# ----
# -----
addOpt
<-
function
(
p
)
{
p
<-
p
+
xlab
(
' Time after AO (min)'
)
+
scale_x_continuous
(
expand
=
c
(
0
,
0
),
limits
=
c
(
0
,
120
),
breaks
=
seq
(
0
,
120
,
20
))
+
scale_y_continuous
(
expand
=
c
(
0
,
0
),
limits
=
c
(
0
,
13
),
breaks
=
seq
(
0
,
13
,
4
))
+
theme_classic
(
base_size
=
8
)
+
theme
(
legend.position
=
'none'
,
axis.line.x
=
element_line
(
color
=
"black"
,
size
=
0.5
),
axis.line.y
=
element_line
(
color
=
"black"
,
size
=
0.5
))
+
theme
(
axis.text.x
=
element_text
(
size
=
8
),
axis.text.y
=
element_text
(
size
=
8
),
plot.margin
=
unit
(
c
(
5
,
5
,
0
,
0
),
"mm"
))
return
(
p
)
}
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/expdata/emdata'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\expdata\\emdata'
)
}
denData
=
read.csv
(
'density_innercore.txt'
,
skip
=
0
,
sep
=
'\t'
)
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
fnames
=
c
(
'delayedMaturation_v0_ts10_den.txt'
,
'delayedMaturation_noPrecursor_ts10_den.txt'
,
'delayedMaturationExponentialV_noPrecursor_ts10_v0.015_den.txt'
,
'delayedMaturation_v0.015_ts10_den.txt'
,
'delayedMaturationExponentialV_ts10_v0.015_den.txt'
)
varNames
=
c
(
'Var 1'
,
'Var 2'
,
'Var 3'
,
'Var 1+2'
,
'Var 1+3'
)
inData
=
list
()
seq_plot
=
c
(
1
,
2
,
3
,
4
,
5
)
for
(
i
in
seq_along
(
fnames
)
)
{
tmpCsv
=
read.csv
(
fnames
[
i
],
skip
=
0
,
sep
=
'\t'
)
tmpCsv
[
'model'
]
=
varNames
[
i
]
tmpCsv
[
'nrpar'
]
=
nrpar
[
i
]
inData
=
rbind
(
inData
,
tmpCsv
)
}
inData
$
model
=
factor
(
inData
$
model
,
levels
=
varNames
[
seq_plot
])
# ----
pint_inter
<-
ggplot
()
+
geom_bar
(
data
=
denData
,
stat
=
'identity'
,
width
=
1.5
,
aes
(
time
,
int_avg
,
fill
=
'red'
))
+
geom_line
(
data
=
inData
,
size
=
0.8
,
aes
(
time
,
inter_i
,
group
=
model
,
colour
=
model
))
+
ylab
(
expression
(
paste
(
"Intermediate density (pores/"
,
mu
,
m
^
2
,
")"
)))
pint_mature
<-
ggplot
()
+
geom_bar
(
data
=
denData
,
stat
=
'identity'
,
width
=
2
,
aes
(
time
,
mat_avg
,
fill
=
'#1E477E'
))
+
geom_line
(
data
=
inData
,
size
=
0.8
,
aes
(
time
,
mature_i
,
group
=
model
,
colour
=
model
))
+
ylab
(
expression
(
paste
(
"Mature density (pores/"
,
mu
,
m
^
2
,
")"
)))
pint_inter
<-
addOpt
(
pint_inter
)
+
scale_fill_manual
(
values
=
c
(
'red'
))
pint_mature
<-
addOpt
(
pint_mature
)
+
scale_fill_manual
(
values
=
c
(
'#1E477E'
))
pint_inter
pint_mature
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\figures'
)
}
ggsave
(
filename
=
"prodVariants_inter_inner_den.pdf"
,
plot
=
pint_inter
,
width
=
71
,
height
=
44
,
units
=
'mm'
)
ggsave
(
filename
=
"prodVariants_mature_inner_den.pdf"
,
plot
=
pint_mature
,
width
=
71
,
height
=
44
,
units
=
'mm'
)
rcode/prodVariants_den.R
0 → 100644
View file @
a3e6801d
library
(
"ggplot2"
)
# ----
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
setwd
(
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
)
}
else
{
setwd
(
'C:\\Users\\toni\\Dropbox\\NPCMaturation\\results\\emdata\\delay'
)
}
fnames
=
c
(
'delayedMaturation_v0_ts10_den.txt'
,
'delayedMaturation_noPrecursor_ts10_den.txt'
,
'delayedMaturationExponentialV_noPrecursor_ts10_v0.015_den.txt'
,
'delayedMaturation_v0.015_ts10_den.txt'
,
'delayedMaturationExponentialV_ts10_v0.015_den.txt'
)
rcode/prodVariants_reduced.R
0 → 100644
View file @
a3e6801d
# ----
library
(
"ggplot2"
)
if
(
Sys.info
()[
'sysname'
]
==
'Darwin'
){
indatadir
<-
'/Users/toni/Dropbox/NPCMaturation/expdata/emdata'
indir
<-
'/Users/toni/Dropbox/NPCMaturation/results/emdata/delay'
outdir
<-
'/Users/toni/Dropbox/NPCMaturation/results/emdata/figures'