R Notebook

---

library(ggplot2)
library(pheatmap)
library(RColorBrewer)
library(tidyverse)
library(ggpubr)
library(ggsignif)
library(openxlsx)
library(viridis)
library(jcolors)
library(stringr)

setwd("//atlas.uni.lux/users/isabel.rosety/GBA/GCase activity/Plots")

The working directory was changed to //atlas.uni.lux/users/isabel.rosety/GBA/GCase activity/Plots inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.

data  <- read_excel("//atlas.uni.lux/LCSB_Cellular_Biology/16-Our Papers/In Preparation/GBA hMO_Isabel/Figures/Fig1/Partials/B//Quantification/20210910_GCase activity results.xlsx",sheet=3)

#Normalize to mean of controls for one feature
dataN <-data %>%
     group_by(Batch, Condition) %>%
     mutate(Gcase_activity=Gcase_activity/mean(data$Gcase_activity[data$Condition=="CTRL"]/100,na.rm = TRUE)) 
write.csv(dataN, file = 'Data as Percentage of controls.csv')

dataN <- read.csv("Data as Percentage of controls.csv")

dataN<-as.data.frame(dataN)

Plot for one feature

dataN%>%
  ggplot(aes(x = Condition, y=Gcase_activity),ordered=TRUE)+
    geom_boxplot(aes(fill=Condition),show.legend = FALSE,width=0.7)+
        #scale_fill_manual(values=c("#2171b5","#B22222","#008B8B"))+  #blue and red
  

scale_fill_manual(values= c("#FFFFFF","#999999"),name = "Condition", guide = "none")+ #guide false will remove the legend for the condition
  #ylim(4,9)+
    #geom_boxplot(width=0.07, fill="white") + 
    geom_point(aes(color=CellLine),size=3,show.legend = T,alpha = 0.5)+
    #scale_color_manual(values = rev(brewer.pal(n=6, name="OrRd")))+
    scale_color_jcolors("pal7")+
    #scale_color_viridis(option = "D", discrete=TRUE)+
    #geom_point(shape = 1,size = 3,colour = "black")+
    theme(legend.key=element_blank()) +
    
  geom_signif(comparisons = list(c("CTRL", "GBA-PD")), test='wilcox.test',
              vjust=0.5, size=0.5, textsize=9, map_signif_level=c("***"=0.001, "**"=0.01, "*"=0.05,  " "=2) ) +
  #facet_grid(~fct_relevel(Day, "d30","d60"), scales="free") +
       labs(x     ="",
        y     = "Relative GCase activity",
       fill  = "Condition",
      title = "GCase activity") +
  theme_bw() +
  theme(
    axis.line = element_line(colour = 'black', size = 1) ,
    axis.title.x = element_blank(),
    axis.text.x = element_text(size=21, color="black"),
    axis.title.y = element_text(size = 21),
    axis.text.y = element_text(size=15, color="black"),
    axis.ticks.y = element_line(),
    axis.ticks.length=unit(.25, "cm"),
     #change legend text font size)
    #legend.key.size = unit(0.7, "cm"),
    #legend.key.width = unit(0.6,"cm"),
    legend.key=element_blank(),
    panel.grid.major = element_blank(), 
    panel.grid.minor = element_blank(),
    panel.border = element_blank(),
    plot.title = element_text(size = 20, hjust=0.5, vjust= 1, face = "bold"),
    plot.subtitle = element_blank(),#element_text(size = 2, hjust=0.5)
    strip.text = element_text(size=12, vjust=0.5),
    strip.background = element_rect(fill="lightgray"),
   # panel.border = element_rect(fill = NA, color = "black"),
    panel.spacing.y = unit(0.8, "lines"),
    strip.switch.pad.wrap=unit(20, "lines"),
    legend.position="right",
    legend.text = element_text(size=17),
    legend.title = element_text(size=19)
    
  )  -> p

  print(p)

#ggsave(paste0(Sys.Date()," GCase activity DIV30.pdf"),height=4)