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fix: transform ANI matrix to 1-D condensed distance matrix #20

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fix: transform ANI matrix to 1-D condensed distance matrix #20

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3 changes: 2 additions & 1 deletion src/aniclustermap/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import seaborn as sns
from matplotlib.colors import BoundaryNorm
from matplotlib.colors import LinearSegmentedColormap as LSC
from scipy.spatial.distance import squareform
from seaborn.matrix import ClusterGrid


Expand Down Expand Up @@ -59,7 +60,7 @@ def clustermap(
ani_matrix_df = pd.read_csv(ani_matrix_df, sep="\t", encoding="utf-8")

if linkage is None:
linkage = hc.linkage(ani_matrix_df, method="average")
linkage = hc.linkage(squareform(100 - ani_matrix_df), method="average")

if cmap_colors is None:
cmap_colors = ["lime", "yellow", "red"]
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3 changes: 2 additions & 1 deletion src/aniclustermap/scripts/aniclustermap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import pandas as pd
import scipy.cluster.hierarchy as hc
import typer
from scipy.spatial.distance import squareform
from typer import Option, Typer

from aniclustermap import __version__, const
Expand Down Expand Up @@ -172,7 +173,7 @@ def cli(

# Hierarchical clustering ANI matrix
logger.info(f"Clustering {mode.value} ANI matrix by scipy UPGMA method")
linkage = hc.linkage(ani_matrix_df, method="average")
linkage = hc.linkage(squareform(100 - ani_matrix_df), method="average")
dendrogram_newick_file = outdir / "ANIclustermap_dendrogram.nwk"
to_newick_tree(ani_matrix_df, linkage, dendrogram_newick_file)
logger.info("Write newick format cluster dendrogram")
Expand Down