def plot_pairwise_dist(self, labels=None, ax=None, cmap=None, cdict=None, metric="euclidean"):
        """
        Plot pairwise distances between all samples

        labels: bool or list
                by default labels aren't included. If labels == True, then labels are read in
                from the vcf file. Alternatively, labels can be passed in as a list, should
                be same length as the number of samples.
        """
        allele_counts = self.genotypes.to_n_alt()
        dist = allel.pairwise_distance(allele_counts, metric=metric)
        if not ax:
            fig = plt.figure(figsize=(5, 5))
            ax = fig.add_subplot(1, 1, 1)

        if isinstance(labels, bool):
            if labels:
                labels = list(self.samples_vcforder)
        elif isinstance(labels, type(None)):
            pass
        else:
            ## If not bool or None (default), then check to make sure the list passed in
            ## is the right length
            if not len(labels) == len(self.samples_vcforder):
                raise IPyradError(LABELS_LENGTH_ERROR.format(len(labels), len(self.samples_vcforder)))

        allel.plot.pairwise_distance(dist, labels=labels, ax=ax, colorbar=False)
def plot_pairwise_dist(self, labels=None, ax=None, cmap=None, cdict=None, metric="euclidean"):
        """
        Plot pairwise distances between all samples

        labels: bool or list
                by default labels aren't included. If labels == True, then labels are read in
                from the vcf file. Alternatively, labels can be passed in as a list, should
                be same length as the number of samples.
        """
        allele_counts = self.genotypes.to_n_alt()
        dist = allel.pairwise_distance(allele_counts, metric=metric)
        if not ax:
            fig = plt.figure(figsize=(5, 5))
            ax = fig.add_subplot(1, 1, 1)

        if isinstance(labels, bool):
            if labels:
                labels = list(self.samples_vcforder)
        elif isinstance(labels, type(None)):
            pass
        else:
            ## If not bool or None (default), then check to make sure the list passed in
            ## is the right length
            if not len(labels) == len(self.samples_vcforder):
                raise IPyradError(LABELS_LENGTH_ERROR.format(len(labels), len(self.samples_vcforder)))

        allel.plot.pairwise_distance(dist, labels=labels, ax=ax, colorbar=False)
def plot_pairwise_dist ( self , labels = None , ax = None , cmap = None , cdict = None , metric = "euclidean" ) : allele_counts = self . genotypes . to_n_alt ( ) dist = allel . pairwise_distance ( allele_counts , metric = metric ) if not ax : fig = plt . figure ( figsize = ( 5 , 5 ) ) ax = fig . add_subplot ( 1 , 1 , 1 ) if isinstance ( labels , bool ) : if labels : labels = list ( self . samples_vcforder ) elif isinstance ( labels , type ( None ) ) : pass else : ## If not bool or None (default), then check to make sure the list passed in ## is the right length if not len ( labels ) == len ( self . samples_vcforder ) : raise IPyradError ( LABELS_LENGTH_ERROR . format ( len ( labels ) , len ( self . samples_vcforder ) ) ) allel . plot . pairwise_distance ( dist , labels = labels , ax = ax , colorbar = False )
Plot pairwise distances between all samples

        labels: bool or list
                by default labels aren't included. If labels == True, then labels are read in
                from the vcf file. Alternatively, labels can be passed in as a list, should
                be same length as the number of samples.
Plot pairwise distances between all samples