TPH2 KO statistics
Alex Meng, Joanes Grandjean
Setup environement
Download DABEST
# you just need to run these once.
install.packages('devtools')
install.pacakges("reshape2")
install.pacakges("wesanderson")
install.packages("svglite")
install.packages("ggpubr")
devtools::install_github("ACCLAB/dabestr")
devtools::install_github("karthik/wesanderson")Load pacakges
library(tidyverse)
library(glue)
library(dabestr)
library(wesanderson) # see https://github.com/karthik/wesanderson
library(reshape2)
library(svglite)
library(ggpubr)
pal <- wes_palette("Darjeeling1")###behavioural tests EPM (Fig1) ##Fig1 dataset description: A. Open arms duration B. Number of entry into closed arms C. Latency time for first time entering open arms D. Total distance moved
#Fig1A
df <- read_csv('assets/tables/EPM_open_arms_duration.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig1A<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "duration in open arms (%)")
ggsave('assets/figure/Fig1A.svg', plot = Fig1A, device = 'svg',dpi = 300)
Fig1A
dabest_hedges$result %>% mutate(p = p_tmp)#Fig1B
df <- read_csv('assets/tables/EPM_entry_closed_arms.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig1B<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "number of entry")
ggsave('assets/figure/Fig1B.svg', plot = Fig1B, device = 'svg',dpi = 300)
Fig1B
dabest_hedges$result %>% mutate(p = p_tmp)#Fig1C
df <- read_csv('assets/tables/EPM_first_time_entry.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig1C<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "latency time (s)")
ggsave('assets/figure/Fig1C.svg', plot = Fig1C, device = 'svg',dpi = 300)
Fig1C
dabest_hedges$result %>% mutate(p = p_tmp)#Fig1D
df <- read_csv('assets/tables/EPM_total_distance.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig1D<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "total distance moved (cm)")
ggsave('assets/figure/Fig1D.svg', plot = Fig1D, device = 'svg',dpi = 300)
Fig1D
dabest_hedges$result %>% mutate(p = p_tmp)###behavioural tests Social interaction (Fig2) ##Fig2 dataset description: A. Experimental diagram B. Total no contact C. Total mounting D. Total aggressiveness
#Fig2B
df <- read_csv('assets/tables/SI_total_no_contact.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig2B<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "total no contact (%)")
ggsave('assets/figure/Fig2B.svg', plot = Fig2B, device = 'svg',dpi = 300)
Fig2B
dabest_hedges$result %>% mutate(p = p_tmp)#Fig2C
df <- read_csv('assets/tables/SI_total_mounting.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig2C<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "total mounting (%)")
ggsave('assets/figure/Fig2C.svg', plot = Fig2C, device = 'svg',dpi = 300)
Fig2C
dabest_hedges$result %>% mutate(p = p_tmp)#Fig2D
df <- read_csv('assets/tables/SI_total_aggressiveness.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2+/-'],var.equal=TRUE)$p.value, t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2+/-','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
Fig2D<-plot(dabest_hedges, palette = pal, rawplot.ylabel = "total aggressiveness (%)")
ggsave('assets/figure/Fig2D.svg', plot = Fig2D, device = 'svg',dpi = 300)
Fig2D
dabest_hedges$result %>% mutate(p = p_tmp)###Expression of oxytocin & receptors (Fig3) ##Fig3 dataset description: A: Diagram of brain punching position B. Prelimbic cortex C. Ventral CA1 region of hippocampus D. Ventral CA3 region of hippocampus E. Dorsal raphe nucleus F. Medial frontal cortex G. Hippocampus H. Paraventricular thalamic nucleus I. Central amygdala nucleus
#Fig3B
df <- read_csv('assets/tables/PCR_PRL.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3B <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "mRNA level (% vs Tph2+/+)")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3B.svg', plot = Fig3B, device = 'svg',dpi = 300)#Fig3C
df <- read_csv('assets/tables/PCR_vCA1.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3C <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "mRNA level (% vs Tph2+/+)")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3C.svg', plot = Fig3C, device = 'svg',dpi = 300)#Fig3D
df <- read_csv('assets/tables/PCR_vCA3.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3D <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "mRNA level (% vs Tph2+/+)")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3D.svg', plot = Fig3D, device = 'svg',dpi = 300)#Fig3E
df <- read_csv('assets/tables/PCR_DR.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3E <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "mRNA level (% vs Tph2+/+)")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3E.svg', plot = Fig3E, device = 'svg',dpi = 300)#Fig3F
df <- read_csv('assets/tables/OXY_MFC.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3F <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "pg oxytocin/µg tissue protein/ml")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3F.svg', plot = Fig3F, device = 'svg',dpi = 300)#Fig3G
df <- read_csv('assets/tables/OXY_HIP.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3G <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "pg oxytocin/µg tissue protein/ml")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3G.svg', plot = Fig3G, device = 'svg',dpi = 300)#Fig3H
df <- read_csv('assets/tables/OXY_PVN.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3H <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "pg oxytocin/µg tissue protein/ml")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3H.svg', plot = Fig3H, device = 'svg',dpi = 300)#Fig3I
df <- read_csv('assets/tables/OXY_CA.csv', col_types = cols()) %>% melt() %>% dplyr::rename(group = variable) %>% drop_na()
df %>% group_by(group) %>% summarise(mean=round(mean(value),2), sd=round(sd(value),2))
dabest_hedges <- dabest(df, group, value, idx = c('Tph2+/+','Tph2-/-'), paired = FALSE) %>% hedges_g()
dabest_hedges
plot(dabest_hedges, palette = pal)
Fig3I <- plot(dabest_hedges, palette = pal, rawplot.ylabel = "pg oxytocin/µg tissue protein/ml")
p_tmp<- c(t.test(df$value[df$group == 'Tph2+/+'], df$value[df$group == 'Tph2-/-'],var.equal=TRUE)$p.value)
dabest_hedges$result %>% mutate(p = p_tmp)
ggsave('assets/figure/Fig3I.svg', plot = Fig3I, device = 'svg',dpi = 300)