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")

Warning: 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)

dataNBarPlot<-dataN%>%
  group_by(CellLine)%>%
  summarise(Mean = mean(Gcase_activity), sd_rating = sd(Gcase_activity))

Error in group_by(., CellLine) : object 'dataN' not found

Violin Plots

dataN%>%
  ggplot(aes(x = Condition, y=Gcase_activity),ordered=TRUE)+
  #geom_violin( aes(fill=Condition),show.legend = T, trim=T),
  geom_violin( aes(fill=Condition),show.legend = T,scale = "width", trim=F)+
  geom_dotplot(binaxis = "y",stackdir = "center",dotsize=0.8)+
  #scale_fill_manual(values= c("#bdd7e7","#2171b5"),name = "Condition", guide = FALSE)+
    scale_fill_manual(values= alpha(c("#1565C0","#CC0000"),0.75),name = "Condition",guide = "none")+
    theme(legend.key=element_blank()) +
    
  geom_signif(comparisons = list(c("CTRL", "GBA-PD")), test='wilcox.test',
              margin_top=0.5,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 = 0.5) ,
    axis.title.x = element_blank(),
    axis.text.x = element_text(size=16, color="black"),
    axis.title.y = element_text(size = 16),
    axis.text.y = element_text(size=10, color="black"),
    axis.ticks.y = element_line(),
    axis.ticks.length=unit(.20, "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
  #t<- cowplot::ggdraw(cowplot::add_sub(p, "Wilcox-test, ***p=0.001, **p=0.01, *p=0.05",hjust=-0.2, size=13))
  print(p)
  ##ggsave(paste0(Sys.Date(),"_", names[i], ".pdf"), plot=t)


ggsave(paste0(Sys.Date()," GCase activity DIV30.pdf"),height=2.5,width=3)

Cell Lines

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)

Bar Plots for all the features one timepoint

dataNBarPlot%>%
  ggplot(aes(x=factor(CellLine, level = c("CTRL1", "CTRL2","CTRL3", "PD1", "PD2","PD3")), y=MeanGCase),ordered=TRUE)+
  #geom_violin( aes(fill=Condition),show.legend = T, trim=T),
  geom_bar(aes(fill=CellLine),stat="summary",position=position_dodge(),colour="black",size=0.3,width=0.8) +
  scale_y_continuous(expand = c(0, 0))+
    scale_fill_manual(values= c("#1565C0", alpha(("#1565C0"),0.7),alpha(("#1565C0"),0.4),"#CC0000", alpha(("#CC0000"),0.5),alpha(("#CC0000"),0.2)),name = "CellLine",guide = "none")+
  geom_errorbar(aes(ymin=MeanGCase, ymax=MeanGCase+sd_rating),width=.2,position=position_dodge(.9), size=0.3)+        # Width of the error bars
    theme(legend.key=element_blank()) +
    
  geom_signif(comparisons = list(c("CTRL", "GBA-PD")), test='wilcox.test',
              margin_top=0.5,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  = "",
      title = "") +
  theme_bw() +
  theme(
   axis.line = element_line(colour = 'black', size = 0.3) ,
    axis.title.x = element_blank(),
    axis.text.x = element_text(size=7, color="black"),
    axis.title.y = element_text(size = 10),
    axis.text.y = element_text(size=7, color="black"),
    axis.ticks.y = element_line(size=0.3),
    axis.ticks.x = element_line(size=0.3),
    axis.ticks.length=unit(.1, "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
  #t<- cowplot::ggdraw(cowplot::add_sub(p, "Wilcox-test, ***p=0.001, **p=0.01, *p=0.05",hjust=-0.2, size=13))
  print(p)
  ##ggsave(paste0(Sys.Date(),"_", names[i], ".pdf"), plot=t)


ggsave(paste0(Sys.Date()," GCase activity DIV30.pdf"),height=2.5,width=3)