ORM_plot

Tools for ORM

script for orm file formating

The purpose of this script is to attribute a "y" value to each fiber to allow them to be plotted in a smart manner, wihtout overlap.

The script starts with a ".gtf" file containing fibers and nucleotides data, and a ".bed" file containing the replicating segments. These two files need to have matching names for each sample:

sample_1.gtf and sample_1.bed ; sample_2.gtf and sample_2.bed ; ...

The final file structure should be a 8 column tab separated file. (See the orm_example.txt file)

• 1st column:

  The feature name: "Fiber", "Segment" or "Nucleotide"

• 2nd column:

  The chromosome of this feature.

• 3rd column:

  The start position of the feature.

• 4th column:

  For features "Fiber" and "Segment", the stop postion.

  For feature "Nucleotide", the fluorescence intensity in arbitray unit, 0 the minimum and 2000 the maximum.

• 5th column:

  The fiber uniq id number.

• 6th and 7th column:

  The Fiber corresponding to the feature start and stop position

• 8th column:

  The y position to plot each feature.

orm_plot

orm_plot is an R function allowing to plot ORM data from formated files (see script to format the files).

• Input file: tab separated 8 columns with the feature type, the chr, the start position, the stop position, the id of the fiber, the start position of the fiber, the stop position of the fiber and the smart y position (see the script to format the files). No header.

• Usage: In R:

  • load the orm file:

     dataset<-read.table("orm_file.txt",header=FALSE)
    

  • load the script:

     source("Path/to/script.R")
    

  • Plot using the chromosome you want, the start position (1000000 by default), the stop position (50000000 by defaut), the orm dataset, the features you want to plot (all by defaut):

     plot_orm(chr="chr1", start=1000000, stop=50000000, dataset=dataset,Fiber=TRUE,Nucleotide=TRUE,Segment=TRUE)