FLAG2A_IF.R

suppressPackageStartupMessages(library(tidyverse))
devtools::load_all('~/Google Drive/My Drive/Scripts/R_packages/myUtilities/')

## ℹ Loading myUtilities

wd <- '~/Google Drive/My Drive/Analysis/METTL2A/'

figdir   <- paste0(wd, 'Figures/FLAG-IF/')
tabledir <- paste0(wd, 'Tables/FLAG-IF/')

Functions

paste_wd <- function(path) {
  paste0(wd, path)
}

Read data

rename_col_and_reshape <- function(df) {
  df |> 
    rename(distance_inches = `Distance_(inches)`) |> 
    pivot_longer(
      cols = -c(distance_inches, sample), 
      names_to = 'channel', values_to = 'intensity'
    )
}

ev_roi1 <- 
  read_csv('FLAG-2A_IF/FLAG4_ROI1.csv' |> paste_wd()) |> 
  mutate(sample = 'FLAG') |> 
  rename_col_and_reshape()

## Rows: 732 Columns: 4
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (4): Distance_(inches), mito, FLAG, DAPI
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

ev_roi1

## # A tibble: 2,196 × 4
##    distance_inches sample channel intensity
##              <dbl> <chr>  <chr>       <dbl>
##  1         0       FLAG   mito       17.4  
##  2         0       FLAG   FLAG        0.730
##  3         0       FLAG   DAPI        0    
##  4         0.00333 FLAG   mito       18.4  
##  5         0.00333 FLAG   FLAG        0.283
##  6         0.00333 FLAG   DAPI        0    
##  7         0.00667 FLAG   mito       18.3  
##  8         0.00667 FLAG   FLAG        0.191
##  9         0.00667 FLAG   DAPI        0    
## 10         0.01    FLAG   mito       17.4  
## # ℹ 2,186 more rows

flag2a_roi2 <- 
  read_csv('FLAG-2A_IF/ROI2_250719.csv' |> paste_wd()) |> 
  mutate(sample = 'FLAG-2A') |> 
  rename_col_and_reshape()

## Rows: 754 Columns: 4
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## dbl (4): Distance_(inches), FLAG, Mito, DAPI
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

flag2a_roi2 

## # A tibble: 2,262 × 4
##    distance_inches sample  channel intensity
##              <dbl> <chr>   <chr>       <dbl>
##  1         0       FLAG-2A FLAG       0.344 
##  2         0       FLAG-2A Mito       0.0006
##  3         0       FLAG-2A DAPI       0     
##  4         0.00333 FLAG-2A FLAG       0.325 
##  5         0.00333 FLAG-2A Mito       0     
##  6         0.00333 FLAG-2A DAPI       0     
##  7         0.00667 FLAG-2A FLAG       0.155 
##  8         0.00667 FLAG-2A Mito       0     
##  9         0.00667 FLAG-2A DAPI       0     
## 10         0.01    FLAG-2A FLAG       0.009 
## # ℹ 2,252 more rows

combined <- 
  bind_rows(ev_roi1, flag2a_roi2) |> 
  mutate(channel = str_replace(channel, 'mito', 'Mito'))
combined

## # A tibble: 4,458 × 4
##    distance_inches sample channel intensity
##              <dbl> <chr>  <chr>       <dbl>
##  1         0       FLAG   Mito       17.4  
##  2         0       FLAG   FLAG        0.730
##  3         0       FLAG   DAPI        0    
##  4         0.00333 FLAG   Mito       18.4  
##  5         0.00333 FLAG   FLAG        0.283
##  6         0.00333 FLAG   DAPI        0    
##  7         0.00667 FLAG   Mito       18.3  
##  8         0.00667 FLAG   FLAG        0.191
##  9         0.00667 FLAG   DAPI        0    
## 10         0.01    FLAG   Mito       17.4  
## # ℹ 4,448 more rows

combined_lineplot <- 
  combined |> 
  ggplot(aes(
    x = distance_inches, y = intensity,
    color = channel
  )) +
  geom_line() +
  scale_x_continuous(breaks = seq(0, 3, 1)) +
  scale_color_manual(values = c('#7777ee', '#22aa22', '#aa22aa')) +
  facet_wrap( ~ sample, axes = 'all')
combined_lineplot |> 
  ggsave_pdf(
    width = 6, height = 4, outdir = figdir
  )