HiC_Aggregate_Plot_Visualization

This repository contains R scripts that streamline the process of generating Hi-C aggregate pileup plots using Coolpuppy from Open2C (https://github.com/open2c/coolpuppy). The scripts automate running coolpup.py, processing its output, and visualizing the results with ggplot2, allowing for easy generation of multiple plots in a single workflow.

Requirements:

Coolpuppy (https://github.com/open2c/coolpuppy) ##Check for other requirements for Coolpuppy R (>=4.4)

R libraries:

library(ggplot2)
library(stringr)
library(reshape2)
library(rhdf5)
library(dplyr)
library(RcolorBrewer)

Input Files

Hi-C file: The script uses mcool files as input, as you will be able to define the resolution required. Bed File: A standard 3,4, or 6 column tab-separated bed file or a tab-separated paired bed file (format: seqnames1,start1,end1,seqnames2,start2,end2).

• Be sure that the syntax of chromsome names are the same as the cooler file. (i.e. "chr1" or "1")
• if using a paired bed file, you will need to change the input paramters (see below)

Functions:

There are three functions available in the script functions.r:

• Local_pileup: Used to create local aggregate pileups (i.e.: region1:region1,region2:region2,region3:region3 etc.)
• Intra_contacts: Used to create aggregate pile-ups of all possible cis contacts
• Inter_contacts: Used to create aggregate pile-ups of all possible trans contacts

Parameters

## PROVIDE PATH TO COOLTOOLS
  path_to_cooltools = "/path/to/coolpup.py"

## PATH TO HIC COOLERS (MCOOL FILES) --> comma separated vector for many files
  cooler=c(
    "/path/to/coolfiles/cooler_sample1.mcool",
    "/path/to/coolfiles/cooler_sample2.mcool",
    "/path/to/coolfiles/cooler_sample3.mcool",
  ) 


## BED FILES TO USE --> comma separated vector for many files
  bed = c(
    "/path/to/bedfiles/peaks_WT.bed",
    "/path/to/bedfiles/peaks_KO.bed"
  )

## BED FILE FORMAT ("bed" OR "bedpe")
  ft_format = "bed" 

## FLANKING WINDOWS IN BASEBAIRS
  flank = 500000 

## RESOLUTION OF HIC COOLER FILE TO USE IN BASEPAIRS
  res = 10000

## OUTPUT FOLDER PATH
  outdir="/path/to/outdir/"

## WEIGHT NAME (e.g. "KR",IF NONE, WRITE "" )
  weight = ""

## NUMBER OF PROCESSORS TO USE,
  proc = 24

## Logical whether to subset the bed files for less processing time
  sample_peaks = T

## if sample_peaks = T, the number of peaks to sample
  sample_number = 1000

Usage

Local Pileups:

library(ggplot2)
library(stringr)
library(reshape2)
library(rhdf5)
library(dplyr)

source("functions.r")


p1 <- Local_pileup(
  path_to_cooltools = "/path/to/coolpup.py",
  cooler=c(
    "/path/to/coolfiles/cooler_sample1.mcool",
    "/path/to/coolfiles/cooler_sample2.mcool",
    "/path/to/coolfiles/cooler_sample3.mcool",
  ) ,
  bed = c(
    "/path/to/bedfiles/peaks_WT.bed",
    "/path/to/bedfiles/peaks_KO.bed"
  ),
  ft_format = "bed" ,
  flank = 500000 ,
  res = 10000,
  outdir="/path/to/outdir/",
  weight = "",
  proc = 24
)

p1

Intra-contact pileups:

library(ggplot2)
library(stringr)
library(reshape2)
library(rhdf5)
library(dplyr)

source("functions.r")

p1 <- Intra_contacts(
  path_to_cooltools = "/path/to/coolpup.py",
  cooler=c(
    "/path/to/coolfiles/cooler_sample1.mcool",
    "/path/to/coolfiles/cooler_sample2.mcool",
    "/path/to/coolfiles/cooler_sample3.mcool",
  ) ,
  bed = c(
    "/path/to/bedfiles/peaks_WT.bed",
    "/path/to/bedfiles/peaks_KO.bed"
  ),
  ft_format = "bed" ,
  flank = 500000 ,
  res = 10000,
  outdir="/path/to/outdir/",
  weight = "",
  proc = 24,
  sample_peaks = T,
  sample_number = 1000
)

p1

Inter-contact pileups:

library(ggplot2)
library(stringr)
library(reshape2)
library(rhdf5)
library(dplyr)

source("functions.r")

p1 <- Inter_contacts(
  path_to_cooltools = "/path/to/coolpup.py",
  cooler=c(
    "/path/to/coolfiles/cooler_sample1.mcool",
    "/path/to/coolfiles/cooler_sample2.mcool",
    "/path/to/coolfiles/cooler_sample3.mcool",
  ) ,
  bed = c(
    "/path/to/bedfiles/peaks_WT.bed",
    "/path/to/bedfiles/peaks_KO.bed"
  ),
  ft_format = "bed" ,
  flank = 500000 ,
  res = 10000,
  outdir="/path/to/outdir/",
  weight = "",
  proc = 24,
  sample_peaks = T,
  sample_number = 500
)

p1