SeqTracks-plot-R

This is a set of functions for creating figures/plots from seqeuncing data

• plot_tl: Generates reads coverage track from TimeLapse experiment showing 0, 1, 2, 3, 4, 5+ mutation contatining reads.
• plot_track: Gerenerates reads coverage track from single sample or overlay of mnultiple samples.
• plot_BarGene: Allows plotting of descrete scale data onto continuous scale annotation.

plot_tl

plot_tl (dir, name, chr, start, end, yscale = NULL, labx = TRUE)

dir     -   directory to serch for .bigWig files
name    -   a unique portion of the file names that selects all mutation track files for both strands e.g. "NMD_rep1"
chr     -   chromosome identifier for plotting window
start   -   start (leftmost) position for plotting window <int>
end     -   end (rightmost) position for plotting window <int>
yscale  -   optional: vector in format c(min,max) for y axis scale (default: autoscale)
labx    -   optional: show genomic coordinates on x axis (default: TRUE)

Example:

 plot_tl("TracksBigwig/Control/", "1hr_1", "chr6", 36592363, 36607600)

plot_tracks

plot_track (dir, name, chr, start, end, yscale = NULL, labx = TRUE, snames = name) 

dir     -   directory to serch for bigWig files
name    -   either single or vector of names to distinguish files  e.g. "NMD_rep1"
chr     -   chromosome identifier for plotting window
start   -   start (leftmost) position for plotting window <int>
end     -   end (rightmost) position for plotting window <int>
yscale  -   optional: vector in format c(min,max) for y axis scale (default: autoscale)
labx    -   optional: show genomic coordinates on x axis (default: TRUE)
snames  -   optional: sample names for leged (default: file name)

Example:

plot_track("TracksBigwig/Control", c("1hr_1.TC.0.pos", "1hr_1.TC.1.pos"), "chr6", 36592363, 36607600)

plot_BarGene

plot_BarGene (name_of_gene, annotation, bar_ylab = "", labx = TRUE)

name_of_gene     -   name of gene for plotting, has to match gene_name column values in annotation
bar_ylab         -   y axis label for barplot (default: off)
labx             -   show genomic coordinates on x axis (default: TRUE)
annotation       -   data.frame used for plotting
                     input is dataframe of exon data from ideally 1 but possibly multiple transcripts
    annotation data.frame has to contain these columns: seqnames, start, end, strand, score, sd, transcript_id, gene_name
    each row has information about a single exon: seqnames      - chromosome name
                                                  start         - leftmost edge of exon
                                                  end           - rightmost edge of exon
                                                  strand        - strand information
                                                  score         - value for barplot
                                                  sd            - value for error bars
                                                  transcript_id - transcript identifier this exon belongs to
                                                  gene_nname    - name of gene this exon belongs to

Example:

plot_BarGene("SRSF3", annot, bar_ylab = "Data +/- SD")

Stacking multiple tracks together

library(patchwork)
p1 <- plot_BarGene("SRSF3", annot, bar_ylab = "Data +/- SD", labx = FALSE)
p2 <- plot_track("TracksBigwig/Control", c("1hr_1.TC.0.pos", "1hr_1.TC.1.pos"), "chr6", 36593781, 36606397, labx = FALSE, snames = c("Sample1", "Sample2"))
p3 <- plot_tl("TracksBigwig/Control/", "1hr_1", "chr6", 36593781, 36606397) + ylab("Sample")

p1 + p2 + p3 + plot_layout(ncol = 1, heights = c(4, 1, 1),  guides = 'collect')