Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Vallo Varik
32drugs
Commits
a809e2b9
Commit
a809e2b9
authored
May 20, 2022
by
Carlota Losa Mediavilla
Browse files
Task1
parent
3a0dee96
Changes
1
Hide whitespace changes
Inline
Side-by-side
Task1.R
0 → 100644
View file @
a809e2b9
library
(
ggplot2
)
library
(
dplyr
)
library
(
tidyverse
)
# EXPLORE
## task1_1
data
<-
read.csv
(
"/Users/carlota/Desktop/EMBL/Vallo_R/01_dat.csv"
,
header
=
TRUE
)
data
%>%
select
(
Well
,
Time_h
,
RawOD
,
uM
)
%>%
ggplot
(
aes
(
y
=
RawOD
,
x
=
Time_h
))
+
geom_line
()
+
labs
(
x
=
"Time (h)"
,
y
=
"Raw OD"
,
title
=
"Growth curves of S.flexneri M90T with Azithromycin"
)
+
facet_wrap
(
~
uM
,
labeller
=
label_both
)
ggsave
(
filename
=
"/Users/carlota/Desktop/EMBL/Vallo_R/plot1_1.pdf"
)
## task1_2
data2
<-
read.csv
(
"/Users/carlota/Desktop/EMBL/Vallo_R/02_dat.csv"
,
header
=
TRUE
)
data2
%>%
select
(
Date
,
Well
,
Time_h
,
RawOD
,
uM
)
%>%
mutate
(
Date
=
as.factor
(
Date
))
%>%
ggplot
(
aes
(
y
=
RawOD
,
x
=
Time_h
,
color
=
Date
))
+
geom_line
()
+
labs
(
x
=
"Time (h)"
,
y
=
"RawOD"
)
+
scale_y_continuous
(
trans
=
"log2"
)
+
# transforms to logarithmic scale
facet_wrap
(
~
uM
,
labeller
=
label_both
)
ggsave
(
filename
=
"/Users/carlota/Desktop/EMBL/Vallo_R/plot1_2.pdf"
)
## task1_3
data3
<-
read.csv
(
"/Users/carlota/Desktop/EMBL/Vallo_R/03_dat.csv"
,
header
=
TRUE
)
data3
%>%
select
(
Date
,
Plt
,
Well
,
Time_h
,
RawOD
,
uM
)
%>%
mutate
(
Date
=
as.factor
(
Date
))
%>%
ggplot
(
aes
(
y
=
RawOD
,
x
=
Time_h
,
color
=
Date
,
group
=
Plt
))
+
# groups according to Plt
geom_line
()
+
labs
(
x
=
"Time (h)"
,
y
=
"RawOD"
)
+
scale_y_continuous
(
trans
=
"log2"
)
+
facet_wrap
(
~
uM
,
labeller
=
label_both
)
ggsave
(
filename
=
"/Users/carlota/Desktop/EMBL/Vallo_R/plot1_3.pdf"
)
# TRANSFORM
## task1_4
data3
<-
read.csv
(
"/Users/carlota/Desktop/EMBL/Vallo_R/03_dat.csv"
,
header
=
TRUE
)
%>%
group_by
(
Date
,
Time_h
,
Plt
)
%>%
#now assign new variables
mutate
(
background
=
RawOD
[
uM
==
-1
],
OD
=
RawOD
-
background
)
#filter(Time_h == 1.08)
#data3$OD <- data3$RawOD - filter(data3, uM == -1)$RawOD
data3
%>%
select
(
Date
,
Plt
,
Well
,
Time_h
,
OD
,
RawOD
,
uM
)
%>%
mutate
(
Date
=
as.factor
(
Date
))
%>%
# is it RawOD or OD?
filter
(
!
str_detect
(
uM
,
"-1"
))
%>%
ggplot
(
aes
(
y
=
OD
,
x
=
Time_h
,
color
=
Date
,
group
=
Plt
))
+
# groups according to Plt
geom_line
()
+
labs
(
x
=
"Time (h)"
,
y
=
"RawOD"
)
+
scale_y_continuous
(
trans
=
"log2"
)
+
facet_wrap
(
~
uM
,
labeller
=
label_both
)
ggsave
(
filename
=
"/Users/carlota/Desktop/EMBL/Vallo_R/plot1_4.pdf"
)
data3
<-
filter
(
data3
,
uM
==
-1
)
%>%
rename
(
bg
=
RawOD
)
%>%
select
(
Date
,
Plt
,
Time_h
,
bg
)
%>%
right_join
(
data3
)
# it matches back based on date, plt and time_h
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment