A note on some of the parameters we are using:
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import genepattern
# import cuzcatlan as cusca
# import pandas as pd
from cuzcatlan import HierarchicalClustering
genepattern.GPUIBuilder(HierarchicalClustering, name="Advanded Hierarchical Clustering.",
description="This function performs hierarchical clustering to group samples (columns) and/or genes (rows) with similar expression profiles.",
parameters={
"pwd": { "hide": True, "default": '.' },
"show": { "hide": True, "default": True },
"col_distance_metric":{
"default": "pearson",
"choices":{'Information Coefficient':"information_coefficient",
'City Block (Manhattan or L1-norm)':'manhattan',
'Euclidean (L2-norm)':"euclidean",
'Pearson Correlation':"pearson",
'Uncentered Pearson Correlation':'uncentered_pearson',
'Uncentered Pearson Correlation, absolute value':'absolute_uncentered_pearson',
'Spearman Correlation':'spearman',
"Kendall's Tau": 'kendall',
'Cosine distance':'cosine',
}
},
"row_distance_metric":{
"default": "pearson",
"choices":{'Information Coefficient':"information_coefficient",
'City Block (Manhattan or L1-norm)':'manhattan',
'Euclidean (L2-norm)':"euclidean",
'Pearson Correlation':"pearson",
'Uncentered Pearson Correlation':'uncentered_pearson',
'Uncentered Pearson Correlation, absolute value':'absolute_uncentered_pearson',
'Spearman Correlation':'spearman',
"Kendall's Tau": 'kendall',
'Cosine distance':'cosine',
}
},
"clustering_method":{
"default": "average",
"choices":{'Pairwise average-linkage':"average",
'Pairwise complete-linkage':'complete',
'Pairwise ward-linkage':'ward',
}
},
"row_centering":{
"default": "Mean",
"choices":{'Subtract the mean from each row':"Mean",
'Subtract the median from each row':'Median',
'No':None,
}
},
"col_centering":{
"default": "Mean",
"choices":{'Subtract the mean from each column':"Mean",
'Subtract the median from each column':'Median',
'No':None,
}
},
"custom_plot":{
"default": "Both",
"choices":{'Plot dendrogram only for samples':"Samples",
'Plot dendrogram only for genes':'Genes',
'Plot dendrogram for both samples and genes':'Both',
}
},
})
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