Generates insertion/deletion plots for each evaluated sample from consensus haplotypes' sequences.
Vector including the paths of files generated by
The list returned by
After execution, a file named
GapsBarPlots.pdf will be saved in the reports folder,
including the plots generated for all samples. In each plot, insertions are represented by red lines
and deletions are represented by blue lines.
This function is designed to be applied at the end of the quality assessment analysis and requires
the previous execution of
from the same package.
## Execute demultiplexing by primer splitDir <- "./splits" splitfiles <- list.files(splitDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE) pm.res <- demultiplexPrimer(splitfiles,samples,primers) ## Obtain consensus haplotypes (default parameters) trimDir <- "./trim" trimfiles <- list.files(trimDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE) int.res <- ConsHaplotypes(trimfiles, pm.res, thr, min.seq.len) ## Apply function mach.Dir <- "./MACH" machfiles <- list.files(mach.Dir,recursive=TRUE, full.names=TRUE, include.dirs=TRUE) PlotInDels(machfiles,pm.res)
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