Skip to content

Display raw sample intensities instead of log2-transformed values #25

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
t0mdavid-m merged 1 commit into from
Apr 29, 2026
+2 −7
Merged

Display raw sample intensities instead of log2-transformed values #25

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 2 additions & 7 deletions content/results_abundance.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
"""Abundance (ProteomicsLFQ) Results Page."""
import streamlit as st
import pandas as pd
import numpy as np
from pathlib import Path
from src.common.common import page_setup
from src.common.results_helpers import get_workflow_dir, get_abundance_data
Expand Down Expand Up @@ -71,10 +70,7 @@
# Get sample columns (between stats and PeptideSequence)
sample_cols = [c for c in pivot_df.columns if c not in ["ProteinName", "log2FC", "p-value", "PeptideSequence"]]

# Create bar chart column with log2-transformed values
pivot_df["Intensity"] = pivot_df[sample_cols].apply(
lambda row: [np.log2(v + 1) for v in row], axis=1
)
pivot_df["Intensity"] = pivot_df[sample_cols].apply(list, axis=1)

# Reorder columns: place Intensity after p-value
display_cols = ["ProteinName", "log2FC", "p-value", "Intensity"] + sample_cols + ["PeptideSequence"]
Expand All @@ -85,9 +81,8 @@
column_config={
"Intensity": st.column_config.BarChartColumn(
"Intensity",
help="Sample intensities (log2 scale)",
help="Raw sample intensities",
width="small",
y_min=0,
),
},
use_container_width=True,
Expand Down
Loading