plot_conc plots the phasing concordance, see
An acset list created by
A character vector of feature names to include in the plot.
A numerical value giving the amount by which plotting text and
symbols should be magnified relative to the default, see
To assess the success of the phasing one can calculate the degree of
variability remaining if all cells with haplotype 2 are set to haplotype 1.
As a rough measure of this this function calculates the variability as the
number of cells that differ from the inferred haplotype for every gene with
two variants. The differing number of cells per gene we denote as the
inconcordance and the number of cells with identical haplotype to the
inferred haplotype as concordance, see
set_gt_conc for further
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##load dataset invisible(marinov) acset = new_acset(featdata = marinov[['featdata']], refcount = marinov[['refcount']], altcount = marinov[['altcount']], phenodata = marinov[['phenodata']]) ##Call gt acset = call_gt(acset, min_acount = 3, fc = 3) ##Filter variants and genes acset = filter_acset(acset, nmincells = 5, nminvar = 2) ##Phase acset = phase(acset, input = 'gt', weigh = FALSE, method = 'exhaust') ##Calculate the genotype concordance before and after phasing acset = set_gt_conc(acset) ##Plot the genotype concordance before and after phasing acset = plot_conc(acset)
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