From caaa9498c123b15761d181ec3dc10e52fe5c64e5 Mon Sep 17 00:00:00 2001 From: Marie Anselmet <marie.anselmet@pasteur.fr> Date: Thu, 19 Oct 2023 17:05:13 +0200 Subject: [PATCH] Plot more components in PCA --- build/lib/libcodonusage/libcodonusage.py | 8 ++++++-- libcodonusage/libcodonusage.py | 4 ++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/build/lib/libcodonusage/libcodonusage.py b/build/lib/libcodonusage/libcodonusage.py index 430c57e..706b30e 100644 --- a/build/lib/libcodonusage/libcodonusage.py +++ b/build/lib/libcodonusage/libcodonusage.py @@ -470,10 +470,14 @@ To compute codon proportions, we can divide each line by its sum, or, equivalently (and hopefully more efficiently), normalize the data using the "l1" norm (which, for positive-only values amounts to the sum). """) + print("codon_proportions1") + print(codon_counts) codon_proportions = pd.DataFrame( normalize(codon_counts, norm="l1"), index=codon_counts.index, columns=codon_counts.columns) + print("codon_proportions2") + print(codon_proportions) # Doesn't seem to be working: # codon_proportions.style.hide(axis="index") if verbose: @@ -953,10 +957,10 @@ def codon_usage_pca( (fig, axes) = plt.subplots(1, 2, figsize=(16, 8)) sns.scatterplot( data=transformed_data, - x=0, y=1, hue=hue, marker=".", ax=axes[0,0]) + x=0, y=1, hue=hue, marker=".", ax=axes[0]) sns.scatterplot( data=transformed_data, - x=2, y=3, hue=hue, marker=".", ax=axes[0,1]) + x=2, y=3, hue=hue, marker=".", ax=axes[1]) if figs_dir is not None and formats is not None: for ext in formats: diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py index 430c57e..c82cea3 100644 --- a/libcodonusage/libcodonusage.py +++ b/libcodonusage/libcodonusage.py @@ -953,10 +953,10 @@ def codon_usage_pca( (fig, axes) = plt.subplots(1, 2, figsize=(16, 8)) sns.scatterplot( data=transformed_data, - x=0, y=1, hue=hue, marker=".", ax=axes[0,0]) + x=0, y=1, hue=hue, marker=".", ax=axes[0]) sns.scatterplot( data=transformed_data, - x=2, y=3, hue=hue, marker=".", ax=axes[0,1]) + x=2, y=3, hue=hue, marker=".", ax=axes[1]) if figs_dir is not None and formats is not None: for ext in formats: -- GitLab