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updated counts.py with wt seq counts

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Tanushree Tunstall 2021-03-03 11:54:48 +00:00
parent c59e3f178d
commit 8009c3fe3d
2 changed files with 19 additions and 1 deletions
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17
scripts/count.py
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@ -310,3 +310,20 @@ n_stop = tot3/len(meta_data)
n_stop*100 #0.11
all_tot = n_del*100 + n_ins*100 + n_stop*100 #1.2
#%% count pncA WT
wt_gene = meta_data.loc[meta_data[dr_muts_col].str.contains('WT', na = False, regex = True, case = False) | meta_data[other_muts_col].str.contains('WT', na = False, regex = True, case = False) ]
meta_data['muts_and_lineage'] = meta_data[dr_muts_col] + meta_data[other_muts_col] + meta_data['lineage']
wt_gene_v2 = meta_data.loc[meta_data['muts_and_lineage'].str.contains('*WT*lineage1', na = False, regex = True, case = False)]
lin1_wt_gene = wt_gene.loc[wt_gene['lineage'].str.contains('lineage1', na = False, regex = True, case = False)]
dr_lin1 = wt_gene.groupby(['lineage'])[dr_muts_col].apply(lambda x: x[x.str.contains('WT')].count())
other_lin1 = wt_gene.groupby(['lineage'])[other_muts_col].apply(lambda x: x[x.str.contains('WT')].count())
dr_lin1_v2 = wt_gene.groupby(['lineage'])[dr_muts_col].value_counts()
other_lin1_v2 = wt_gene.groupby(['lineage'])[other_muts_col].value_counts()

3
scripts/plotting/ggcorr_all_PS_LIG.R
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@ -221,7 +221,8 @@ head(my_ggcorr_ps)
corr1 <- round(cor(my_ggcorr_ps, method = "spearman", use = "pairwise.complete.obs"), 1)
# p-value matrix
pmat1 <- cor_pmat(my_ggcorr_ps, method = "spearman", use = "pairwise.complete.obs")
pmat1 <- cor_pmat(my_ggcorr_ps, method = "spearman", use = "pairwise.complete.obs"
, conf.level = 0.99)
corr2 = psych::corr.test(my_ggcorr_ps
, method = "spearman"