added generate_tree function to Kinome object

[harinlee83]

Added

• New feature for generating kinome tree using same logic as website. Original kinome tree SVG sourced from CORAL

Example Usage for Single Site

import kinase_library as kl

df = kl.Substrate('PSVEPPLsQETFSDL').predict()
# Sort the top 30 results
df = df.head(30)

kl.utils.generate_tree(df, "output/score_site_tree.svg", "Percentile", { "high": 100,  "middle": 90, "low": 60 })

Example Usage for Fisher Enrichment Results

enrichment_df =  pd.read_csv("../differential_enrichment_example_file.tsv", sep="\t")
diff_phos = kl.DiffPhosData(enrichment_df,lfc_col='logFC', seq_col='Sequence', pval_thresh=0.1, lfc_thresh=1)
en_res = diff_phos.kinase_enrichment(kin_type='ser_thr', kl_method='percentile_rank', kl_thresh=15)
en_res.generate_tree("output/diff_phos_tree.svg")

Example Usage for Binary Enrichment Results

raw_predetermined_foreground_sequences = pd.read_csv("../predetermined_enrichment_foreground_example_file.tsv", sep="\t")
raw_predetermined_background_sequences = pd.read_csv("../predetermined_enrichment_background_example_file.tsv", sep="\t")
kinase_enrichment_data = kl.EnrichmentData(
        raw_predetermined_foreground_sequences, raw_predetermined_background_sequences, fg_seq_col="Foreground",
        bg_seq_col="Background")
enrichment_results = kinase_enrichment_data.kinase_enrichment(non_canonical=False,
                                                                kl_method='percentile_rank', kl_thresh=15, kin_type='ser_thr')
enrichment_results.generate_tree("output/binary_enrichment_tree.svg")

Example Usage for Motif Enrichment Analysis Results

raw_geneset_enrichment_sequences = pd.read_csv("../geneset_enrichment_example_file.tsv", sep="\t")
me_data = kl.RankedPhosData(raw_geneset_enrichment_sequences, rank_col="Ranking", seq_col="Sequence")
enrichment_results = me_data.mea(kin_type='ser_thr', kl_method='percentile_rank', kl_thresh=15, non_canonical=False)
enrichment_results.generate_tree("output/mea_tree.svg")

[yaront]

Closes #50