RosaBioinfo

Quantitative analysis of WO phage induction assays

January 26, 2026

Alice Brunner

Language: R

Notebook setup

Packages

# Packages

library(ggplot2)   
library(readxl)   
library(ggpubr)   
library(lme4)
library(emmeans)  
library(DHARMa)    
library(performance) 
library(tidyr)

Data

The following files: Data/induction_slab_results.xlsx and Data/induction_mito_slab_R_results.xlsx are required.

# Data

Temp_data <- read_excel('Data/induction_slab_results.xlsx')

Mito_data <- read_excel('Data/induction_mito_slab_R_results.xlsx')

Temperature treatment

This section presents the qPCR-based quantification of Wolbachia and WO phage abundance following thermal induction of adult SLAB females. Statistical comparisons between treated and control groups were performed using Wilcoxon rank-sum tests.

Plot on Wolbachia

#  Transformation de la variable "statut" en facteur avec un ordre spécifique
Temp_data$statut <- factor(Temp_data$type_induction, levels = c("temp_37_1H", "Control"))

#  Création d’un boxplot pour visualiser la quantité de *Wolbachia*
ggplot(Temp_data, aes(x = type_induction, y = wsp_ace2, fill = type_induction)) +
  geom_boxplot() +
  geom_jitter(position = position_jitter(0.2), size = 2, alpha = 0.6, color = "black") +
  theme_classic() +
  labs(title = "Quantity of Wolbachia depending on induction",
       x = "Experimental condition",
       y = "Wolbachia/Mosquito cells (WSP/ACE2)") +
  theme(legend.position = "none")

Figure 3B.1 | Effect of thermal induction on *Wolbachia* abundance. *Wolbachia* abundance (wsp/ace2) measured by qPCR in adult SLAB females exposed to 37 °C for 1 h compared with control females maintained at 27 °C. Each point represents one individual; boxes show median and interquartile range.

ggsave(
  filename = "Output/Figure_3B_1_wsp_temperature.png",
  width = 6, height = 4, dpi = 300
)

Plot on Phage WO

#  Plot WO

ggplot(Temp_data, aes(x = type_induction, y = gpw_ace2, fill = type_induction)) +
  geom_boxplot() +
  geom_jitter(position = position_jitter(0.2), size = 2, alpha = 0.6, color = "black") +
  theme_classic() +
  labs(title = "Quantity of Wolbachia phage depending on induction",
       x = "Experimental condition",
       y = "phage/Mosquito cells (gpw/ACE2)") +
  theme(legend.position = "none")

Figure 3B.1 | Effect of thermal induction on WO abundance. WO abundance (gpw/ace2) measured by qPCR in adult SLAB females exposed to 37 °C for 1 h compared with control females maintained at 27 °C. Each point represents one individual; boxes show median and interquartile range.

ggsave(
  filename = "Output/Figure_3B_1_WO_temperature.png",
  width = 6, height = 4, dpi = 300
)

Stats on Wolbachia

wilcox_wsp <- wilcox.test(
  wsp_ace2 ~ type_induction,
  data = Temp_data,
  exact = FALSE
)

wilcox_wsp

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  wsp_ace2 by type_induction
## W = 22, p-value = 0.5892
## alternative hypothesis: true location shift is not equal to 0

Stats on Phage

wilcox_gpw <- wilcox.test(
  gpw_ace2 ~ type_induction,
  data = Temp_data,
  exact = FALSE
)

wilcox_gpw

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  gpw_ace2 by type_induction
## W = 22, p-value = 0.5892
## alternative hypothesis: true location shift is not equal to 0

Mitomycine treatment

This section presents qPCR quantifications following chemical induction of first-instar SLAB larvae exposed to mitomycin C (5 ng ml⁻¹) for four days.

Plot on Wolbachia

Mito_data$statut <- factor(Mito_data$type_induction, levels = c("Mitomycine_4d", "Control"))

ggplot(Mito_data, aes(x = type_induction, y = wsp_ace2, fill = type_induction)) +
  geom_boxplot() +
  geom_jitter(position = position_jitter(0.2), size = 2, alpha = 0.6, color = "black") +
  theme_classic() +
  labs(title = "Quantity of Wolbachia depending on induction",
       x = "Experimental condition",
       y = "Wolbachia/Mosquito cells (WSP/ACE2)") +
  theme(legend.position = "none")

Figure 3B.2 | Effect of mitomycin C treatment on *Wolbachia* abundance. *Wolbachia* abundance (wsp/ace2) measured by qPCR in first-instar (L1) SLAB larvae exposed to mitomycin C (5 ng ml⁻¹) for four days compared with untreated control larvae. Each point represents one individual; boxes show median and interquartile range.

ggsave(
  filename = "Output/Figure_3B_2_Wolbachia_temperature.png",
  width = 6, height = 4, dpi = 300
)

Plot on Phage WO

ggplot(Mito_data, aes(x = type_induction, y = gpw_ace2, fill = type_induction)) +
  geom_boxplot() +
  geom_jitter(position = position_jitter(0.2), size = 2, alpha = 0.6, color = "black") +
  theme_classic() +
  labs(title = "Quantity of Wolbachia phage depending on induction",
       x = "Experimental condition",
       y = "phage/Mosquito cells (gpw/ACE2)") +
  theme(legend.position = "none")

Figure 3B.2 | Effect of mitomycin C treatment on WO abundance. WO abundance (gpw/ace2) measured by qPCR in first-instar (L1) SLAB larvae exposed to mitomycin C (5 ng ml⁻¹) for four days compared with untreated control larvae. Each point represents one individual; boxes show median and interquartile range.

ggsave(
  filename = "Output/Figure_3B_2_WO_temperature.png",
  width = 6, height = 4, dpi = 300
)

Stats on Wolbachia

wilcox_wsp <- wilcox.test(
  wsp_ace2 ~ type_induction,
  data = Mito_data,
  exact = FALSE
)

wilcox_wsp

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  wsp_ace2 by type_induction
## W = 37, p-value = 0.02681
## alternative hypothesis: true location shift is not equal to 0

Stats on Phage quantities

wilcox_gpw <- wilcox.test(
  gpw_ace2 ~ type_induction,
  data = Mito_data,
  exact = FALSE
)

wilcox_gpw

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  gpw_ace2 by type_induction
## W = 38, p-value = 0.01842
## alternative hypothesis: true location shift is not equal to 0