Example how to compensate imc .txt files using CATALYST

compensate_imc_txt_file.Rmd

---
title: ".txt file image compensation"
author: 'Vito Zanotelli et al.'
output:
  html_document:
    df_print: paged
    keep_md: true
---
# Aim
This shows how to compensate a .txt file using CATALYST

```{r}
library(CATALYST)
library(data.table)
library(ggplot2)
library(flowCore)
library(dplyr)
library(dtplyr)
library(EBImage)
library(fields)
library(viridis)
```


## Helper functions
```{r}
col2img <- function(dat, valcol, xcol='X', ycol='Y'){
  # Converts the image data into a 2D image
  xmax = dat[, max(get(xcol))]
  ymax = dat[, max(get(ycol))]
  # sometimes the last row is incomplete, thus only take the data until the second last row in this case
  if (xmax < dat[, get(xcol)[.N]]){
    ymax = ymax-1
  }
  xmax = xmax+1
  ymax = ymax+1
  
  img = matrix(data=dat[1:(xmax*ymax), get(valcol)], nrow = xmax, ncol = ymax)
  return(img)
}


normimg <- function(x){
  #normalize image for visualization
  xmax = max(x)
  x = x/xmax
  # this removes specle noise
  x = EBImage::medianFilter(x, size=1)
  x = x*xmax
  return(x)
}

get_metals_from_txtname <- function(nam){
  nam =  gsub('.*\\(', '', nam)
  nam = gsub('\\)', '',nam)
  return(nam)
}

#' Estimates spillover directly from a folder containing IMC .txt files
comp_datimg <- function(datimg, sm, method='nnls',...){
  orig_names = colnames(img)
  metal_names = sapply(orig_names, get_metals_from_txtname)
  img_mat = as.matrix(datimg)
  colnames(img_mat) <- metal_names
  
  img_comp = img_mat %>%
    flowCore::flowFrame() %>%
    CATALYST::compCytof(sm, method=method, ...) %>%
    flowCore::exprs() %>%
    as.data.table()
  setnames(img_comp, orig_names)
  return(img_comp)
}
```



## Set paths
```{r}
fn_sm = 'Spillover_Matrix_sm.csv'
fn_img = 'imc_example_image.txt'
fol_out = '.'
fn_out = 'imc_example_comp.txt'
```

## Read img
Fread is the fastest .csv reader I am aware of.
```{r}
img = fread(fn_img,sep = '\t')
```


### Visualization
```{r}
par(mfrow=c(1,2))

col2img(img, 'CarbAnhyd(Er166Di)')  %>%
  normimg() %>%
  fields::image.plot(col=viridis(50))
  
col2img(img, '(Er167Di)')  %>%
  normimg() %>%
  fields::image.plot(col=viridis(50))
```
## Compensate the image

```{r}
sm = read.csv(fn_sm, row.names = 1)

img_comp = comp_datimg(img, sm = sm)

```
### Visualization after compensation
```{r}
par(mfrow=c(1,2))
col2img(img_comp, 'CarbAnhyd(Er166Di)')   %>%
  normimg() %>%
  fields::image.plot(col=viridis(50))
  
col2img(img_comp, '(Er167Di)')  %>%
  normimg() %>%
  fields::image.plot(col=viridis(50))
```
### Write the image file

fwrite is a fast way to write .txt files
```{r}
fwrite(img_comp, file=file.path(fol_out, fn_out),sep='\t')
```

```{r}
sessionInfo()
```