🌻 Strand-seq tri-channel plots

R functions for tri channel plotting of single cell Strand-seq data.

Usage

1. Clone the repository

git clone https://github.com/pweidner/tri-channel-plots

2. Open the run_script.R and run the plot_channels function

To do so you will have to provide the following input files:

• d <- scTRIP counts output file (e.g. HD1.txt.gz)
• d.hap <- run haplotagger on bam files in the /haplotag folder (or import such table after running it once)

Here are some function parameters you can tweak:

• cell_ID (subsets for cells, "i504" or "P1530_i504")
• chromosome (subsets for chr, e.g. "chr2")
• channels (What channels to display: 1=State, 2=Depth, 3=Haps (merged), 4 = Haps (split))
• plot_range (subsets for ranges, e.g. c(40000000,120000000))
• count = FALSE (switches between count plot or W:C ratio, default W:C)
• roi (adds highlight into the plot, e.g. c(7500000,85000000)

Roadmap

📕 Technical features

• Make yaml file for conda env to launch into RStudio server on the cluster
• Option to split H1 and H2 in seperate plots
• Option to plot sv call track along the plotting region
• General option to chose combination of channel plots through numeric ID (e.g. 3=classical trichannel, 4= same but split haps etc.)
• Update ggarrange composition based on channels ID after including merged haps
• Region of interest highlighting
• Add Counts channel (hisogram plot)
• Unified title including set params
• coord_flip = T option to plot horizontal version
• gene = "CD3" param to zoom in on genomic ranges of interest
• margin = 2 param exclusive to plot_range that set a margin to plot around roi/gene
• loop through all cells of samples for given ranges for manual curation of hotspots (sample param)
• parallelization for haplotagger

🛑 Small issues

• filtering for whole chromosomes when plot_range=NULL corrently not working
• Scaling
• Input parameter checks especially for channels beeing either 1,2,3 or 4 for now!
• Formatting of breaks in smaller regions (scale_mb function)
• subsetting is slow

Example output plot:

Authors

• Patrick Weidner
• Suharto Bannerjee
• David Porubsky wrote the bamregion2ranges.R function! :)

📬 Please contact us with any problems or submit them as an issue in this Github repository.