Information

Analysis of yH2AX/RAD51 staining image data for Anna Middleton.
Data stored in I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/

Packages

library(tidyverse)
library(gridExtra)

Import data

IGROV1_0.5Gy <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/IGROV1 0.5Gy/MyExpt_EditedDAPI_IGROV1 0.5Gy.csv")
IGROV1_NoIR <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/IGROV1 No IR/MyExpt_EditedDAPI_IGROV1_No IR.csv")
RPE_0.5Gy <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/RPE 0.5Gy/MyExpt_EditedDAPI_RPE 0.5Gy.csv")
RPE_NoIR <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/RPE No IR/MyExpt_EditedDAPI_RPE No IR.csv")
OVCAR5_0.5Gy <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/OVCAR5 0.5Gy/MyExpt_EditedDAPI_OVCAR 0.5Gy.csv")
OVCAR5_NoIR <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/OVCAR5 No IR/MyExpt_EditedDAPI_OVCAR5 No IR.csv")
PE01_0.5Gy <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/PE01 0.5Gy/MyExpt_EditedDAPI_PE01 0.5Gy.csv")
PE01_NoIR <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/PE01 No IR/MyExpt_EditedDAPI_PE01 No IR.csv")
PE06_0.5Gy <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/PE06 0.5Gy/MyExpt_EditedDAPI_PE06 0.5Gy.csv")
PE06_NoIR <- read.csv("I:/research/jblab/data/shared_folders/light_microscopy/Anna Middleton/28062023 post 4h 0.5Gy gH2AX and RAD51 staining__2023-06-28T11_06_47-Measurement 1/Data analysed/PE06 No IR/MyExpt_EditedDAPI_PE06 No IR.csv")

Merge all data into one data frame

dataFociCounts <- tibble(cell_line="IGROV1",treatment="0.5 Gy",gH2AX=IGROV1_0.5Gy$Children_H2AX_Count,RAD51=IGROV1_0.5Gy$Children_RAD51_Count) %>%
  full_join(tibble(cell_line="IGROV1",treatment="untreated",gH2AX=IGROV1_NoIR$Children_H2AX_Count,RAD51=IGROV1_NoIR$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="RPE",treatment="0.5 Gy",gH2AX=RPE_0.5Gy$Children_H2AX_Count,RAD51=RPE_0.5Gy$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="RPE",treatment="untreated",gH2AX=RPE_NoIR$Children_H2AX_Count,RAD51=RPE_NoIR$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="OVCAR5",treatment="0.5 Gy",gH2AX=OVCAR5_0.5Gy$Children_H2AX_Count,RAD51=OVCAR5_0.5Gy$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="OVCAR5",treatment="untreated",gH2AX=OVCAR5_NoIR$Children_H2AX_Count,RAD51=OVCAR5_NoIR$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="PEO1",treatment="0.5 Gy",gH2AX=PE01_0.5Gy$Children_H2AX_Count,RAD51=PE01_0.5Gy$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="PEO1",treatment="untreated",gH2AX=PE01_NoIR$Children_H2AX_Count,RAD51=PE01_NoIR$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="PEO6",treatment="0.5 Gy",gH2AX=PE06_0.5Gy$Children_H2AX_Count,RAD51=PE06_0.5Gy$Children_RAD51_Count)) %>%
  full_join(tibble(cell_line="PEO6",treatment="untreated",gH2AX=PE06_NoIR$Children_H2AX_Count,RAD51=PE06_NoIR$Children_RAD51_Count))

Plot data

ggplot(dataFociCounts,aes(x=gH2AX,y=RAD51,colour=treatment))+
  geom_point()+
  facet_grid(cols=vars(cell_line),row=vars(treatment))+
  xlab("gH2AX foci counts")+
  ylab("RAD51 foci counts")

#log transform data
ggplot(dataFociCounts,aes(x=gH2AX,y=RAD51,colour=treatment))+
  geom_point()+
  scale_y_continuous(trans="log2")+
  scale_x_continuous(trans="log2")+
  facet_grid(cols=vars(cell_line),row=vars(treatment)) +
  xlab("log2 gH2AX foci counts")+
  ylab("log2 RAD51 foci counts")
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Transformation introduced infinite values in continuous x-axis

ggplot(dataFociCounts,aes(x=gH2AX,y=RAD51,colour=treatment))+
  geom_point()+
  scale_y_continuous(trans="log10")+
  scale_x_continuous(trans="log10")+
  facet_grid(cols=vars(cell_line),row=vars(treatment)) +
  xlab("log10 gH2AX foci counts")+
  ylab("log10 RAD51 foci counts")
## Warning: Transformation introduced infinite values in continuous y-axis
## Transformation introduced infinite values in continuous x-axis