Rgraphs with ggplot
#AMOUNT OF CLONES setwd("~/Documents/experiments/Heat shock") #does not make sense as repository is wd install.packages("readxl") library(readxl)
dat <- read_excel(file.choose())
#directly pick up file: dat <- read_excel('/Users/hd475/Documents/experiments/Heat shock/NB counting.xlsx') View(dat)
install.packages("ggplot2") install.packages("dplyr") library(ggplot2) library(tidyverse) library(ggpubr) library(rstatix) library(dplyr)
#change order and remove NA(use short version of table for this): dat = na.omit(dat) HSrelevel <- fct_relevel(dat$HS, 'none', '1 min', '5 min', '10 min', '20 min', '30 min', '20-60-20', '45 min', '60 min', '90 min', '60-30-60', '120 min', '180 min')
#automatic colors
install.packages("RColorBrewer")
#final graph ggplot(dat, aes(y=Ratio, x=HSrelevel, group=HSrelevel, fill=HSrelevel))+theme_classic()+theme(legend.position="none")+ theme(axis.title.y = element_text(size = 12, face=2))+theme(axis.title.x = element_text(size = 12, face=2))+ scale_fill_brewer(palette='Set3')+ labs(y="Ratio Clones (%)", x="Heat shock (min)")+geom_boxplot()+geom_jitter()+theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
#add stats
#only works with less comparisons (depending on the amount of data) my_comparisons3 <- list(c('none', '45 min'), c('none', '60 min'), c('none', '90 min'))
ggplot(dat, aes(y=Ratio, x=HSrelevel, group=HSrelevel, fill=HSrelevel))+theme_classic()+theme(legend.position="none")+ theme(axis.title.y = element_text(size = 12, face=2))+theme(axis.title.x = element_text(size = 12, face=2))+ scale_fill_brewer(palette='Set3')+ labs(y="Ratio Clones (%)", x="Heat shock (min)")+geom_boxplot()+geom_jitter()+theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+stat_compare_means(comparison=my_comparisons3, method="t.test", aes(label = ..p.signif..))DOT PLOT with colors by group as dots
#ratio dpn RFP
ggplot(dat, aes(y=deadpan, x=clones, color=HSrelevel)) + geom_point(size=2)+ theme_classic()+ theme(axis.title.y = element_text(size = 12, face=2))+theme(axis.title.x = element_text(size = 12, face=2))+ ylim(0,150)+ labs(y="# Deadpan-labelled cells", x="# RFP-labelled cells")+scale_colour_discrete("Heat shock")