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paper.md

@@ -57,15 +57,15 @@ To facilitate comparisons within a set of clusterings, the *CluSim* package prov
 
 
 
-![Evaluating clustering comparisons w.r.t. random models.](paperfigures/CluSimFig1.pdf)
+![Evaluating clustering comparisons w.r.t. random models.](paperfigures/CluSimFig1.png)
 A comparison using the Rand Index between the classification of cancer types and clustering labels derived using Hierarchical Clustering on gene expression data ($0.5$, red). above, Pairwise comparisons between samples from the Permutation model (blue, see [@Hubert1985adjrand]) with mean $0.44$ (black). below, Pairwise comparisons between samples from the one-sided model with a Fixed Number of Clusters (blue, see [@Gates2017impact]) with mean $0.59$ (black). The Permutation model suggests Hierarchical Clustering is more similar to the ground truth than a random clustering, while the one-sized fixed number of clusterings model, the more appropriate model for this scenario, reveals that the result is less similar than random clusterings.
 
 
 
 In the second example, we identify the loci of gene-tree heterogeneity in an analysis of $424$ nuclear genes from $37$ eutherian mammals [@Song2012mammalphylogeny]. Specifically, we perform all pair-wise comparisons between the $424$ phylogenetic trees (dendrograms, exemplified in Fig. 2**a**) derived from individual gene sequence data [@Mirarab2014astral]. The average element-centric similarity between the trees (Fig. 2**b**) reveals their overall similarity, with few conflicts near the roots of the trees (high similarity for the scaling parameter, $r<0$), while decreasing similarity suggest greater conflicts towards the leaves (lower similarity for the scaling parameter,$r>0$). The distribution of element-wise frustration scores over the taxa reveal the loci of greatest gene tree in-congruence (Fig. 2**c**). Specifically, the 8 taxa with lowest frustration correspond to the 5 taxa previously identified with structural discrepancies (bats, shrews, and hedgehog, blue, [@Mirarab2014astral]), and the 3 taxa with the smallest bootstrapping support in the maximum-pseudolikelihood coalescent tree (pig, guinea pig, kangaroo rat, purple, [@Song2012mammalphylogeny]). This comparison provides quantitative insights into the complexities commonly observed in phylogentic data.
 
 
-![Element-centric comparisons of phylogenetic dendrograms.](paperfigures/CluSimFig2.pdf)
+![Element-centric comparisons of phylogenetic dendrograms.](paperfigures/CluSimFig2.png)
 **a**, An example phylogenetic tree for the $37$ mammals from [@Song2012mammalphylogeny]. **b**, The average element-centric similarity between $424$-gene trees for different scaling parameters reveals few conflicts near the roots (left, $r<0$), while decreasing similarity for increasing $r$ suggests greater conflicts towards the leaves (left, $r>0$). **c**, The element-centric frustration highlights the 5 taxa previously identified with structural discrepancies (bats, shrews, and hedgehog, blue, [@Mirarab2014astral]), and the 3 taxa with the smallest bootstrapping support in the maximum-pseudolikelihood coalescent tree (pig, guinea pig, kangaroo rat, purple, [@Song2012mammalphylogeny]).