blab cartography issues

blab / cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2

https://doi.org/10.1101/2024.02.07.579374

MIT License

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Text edits

#117 huddlej opened 4 days ago
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Rerun PCA with simplex encoding of sequences

#116 huddlej opened 5 days ago
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Rerun all PCA and t-SNE analyses with alternate encoding of inputs for PCA

#115 huddlej opened 1 week ago
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Report IQ-TREE parameters in methods

#114 huddlej opened 1 month ago
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Add description of how we plan to use these methods for specific use cases like outbreak response

#113 huddlej opened 1 month ago
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Compare number of cluster-specific mutations to the number of clade-specific mutations

#112 huddlej opened 1 month ago
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Consider defining a metric of cluster confidence based on the number of cluster-specific mutations

#111 huddlej opened 1 month ago
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Assess cluster accuracy compared to Pango lineages for embeddings within a specific SC2 clade

#110 huddlej opened 1 month ago
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Clarify value of including additional gene segments beyond HA/NA for influenza embeddings

#109 huddlej opened 1 month ago
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Add supplemental figure(s) that shows tangletree from Nextstrain between HA and NA colored by MCC and/or t-SNE clusters

#108 huddlej opened 1 month ago
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Clarify sensitivity of methods to homoplasies, reversions, etc. and confidence metrics for clusters

#107 huddlej opened 1 month ago
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Attempt plotting with rectangular tree layout in Altair

#106 huddlej opened 1 month ago
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Remove variable branch widths from tree and embedding figures

#105 huddlej opened 1 month ago
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Cite related network/cluster-based visualization approaches (e.g., MicrobeTrace)

#104 huddlej opened 1 month ago
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Elaborate on contents of supplemental figures and tables in their captions

#103 huddlej opened 1 month ago
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Expand description of simulated populations in results

#102 huddlej opened 1 month ago
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Link to supplemental data files on Zenodo from each supplemental item's caption

#101 huddlej opened 1 month ago
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Test interpretability of tree/embedding figures with alternate color schemes

#100 huddlej opened 1 month ago
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Run HDBSCAN directly on genetic distances and compare clusters to those from embeddings

#99 huddlej opened 1 month ago
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Update preprint files

#98 huddlej opened 2 months ago
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Update cover letter

#97 huddlej closed 2 months ago
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Update LaTeX template

#96 huddlej closed 2 months ago
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Cite additional related work

#95 huddlej closed 2 months ago
1
Report how methods scale with data size

#94 huddlej closed 2 months ago
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Clarify novelty of main results in abstract, intro, results, and discussion

#93 huddlej closed 2 months ago
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Add supplemental figures with cluster vs. genetic group heatmap

#92 huddlej closed 2 months ago
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Add supplemental figures of example SARS-CoV-2 recombination events visualized with MDS

#91 huddlej closed 2 months ago
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Add headers to the discussion

#90 huddlej closed 2 months ago
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Fix boxplot positions to allow gaps between genetic distances on the x-axis

#89 huddlej closed 2 months ago
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Reduce verbosity of the results

#88 huddlej closed 5 months ago
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Reduce verbosity of results

#87 huddlej closed 5 months ago
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Address inadequate justification for optimization metrics of linearity and cluster accuracy

#86 huddlej closed 5 months ago
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Address lack of prescriptive settings for methods applied to new viruses

#85 huddlej closed 5 months ago
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Cover letter

#84 huddlej closed 5 months ago
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Quantify monophyletic clusters

#83 huddlej closed 6 months ago
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Determine the effect of sampling bias (e.g., regional or clade composition bias) on embeddings and cluster accuracy

#82 huddlej closed 5 months ago
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Automate recombinant lineages

#81 huddlej closed 6 months ago
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Calculate branch positions for internal nodes

#80 huddlej closed 6 months ago
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Quantify monophyly of clusters for early/late flu and early SC2 by counting the number of ancestral state switches for each cluster when traversing the tree in preorder

#79 huddlej closed 6 months ago
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Plot embeddings by clade with branches from the phylogeny for early and late H3N2 HA and early SC2 to show how embeddings correspond to phylogeny

#78 huddlej closed 6 months ago
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Use official Pango lineage designation JSON as the source of truth for SARS-CoV-2 recombinant lineages

#77 huddlej closed 6 months ago
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Add early flu embeddings for ancestral sequences

#76 huddlej closed 6 months ago
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Minor manuscript edits

#75 trvrb closed 6 months ago
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Supplemental figures and tables at end of manuscript

#74 trvrb closed 6 months ago
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Methods placement

#73 trvrb closed 6 months ago
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Improve language surrounding Pango

#72 trvrb closed 6 months ago
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Don't version LaTeX manuscript PDF

#71 trvrb closed 6 months ago
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Write "Author Summary"

#70 huddlej closed 5 months ago
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Add workflow to test effects of genetic bias

#69 huddlej closed 5 months ago
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Clean up old source code from cartography repo

#68 huddlej closed 3 months ago
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