Commit a809e2b9 authored by Carlota Losa Mediavilla's avatar Carlota Losa Mediavilla
Browse files

Task1

parent 3a0dee96
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
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