mdhewei/bioinfor-claw/plot-survival

Plot Survival

Purpose

Create professional Kaplan-Meier survival curves for time-to-event data with comprehensive statistical testing and annotations. This skill computes the Kaplan-Meier estimator from raw survival data, performs log-rank and Wilcoxon tests, generates publication-quality plots with confidence intervals, median annotations, at-risk tables, and optional output in PNG and SVG formats.

Use when / Not when

Use when

• You need to visualize time-to-event data (survival, recurrence-free survival, disease-free survival, etc.)
• You want to compare survival between groups (treatment vs. control, responder vs. non-responder)
• You need to test for significant group differences (log-rank or Wilcoxon p-values)
• You're preparing figures for a publication (high-quality, customizable aesthetics)
• You want to stratify by continuous variables (e.g., high vs. low expression, split at median)
• You need confidence intervals and at-risk tables (clinical/biomedical standard)
• You're reporting median survival and survival probabilities at specific time points

Not when

• Your data has competing risks (use competing risks packages like cmprsk)
• You have more than 10-15 groups (plot becomes unreadable; consider binning)
• You need Cox regression or adjusted curves (use survival R package or lifelines Python)
• You have hierarchical data with repeated events per individual (use frailty models)
• Data is left-censored or interval-censored (only right-censoring is supported)
• You need permutation-based p-values (script uses parametric chi-squared approximation)

Expected inputs / outputs

Inputs

• CSV/TSV file with columns:
• Time-to-event (required): numeric, column name specified by --time-col
• Event status (required): 1 = event occurred, 0 = censored
• Group (required for multi-group KM): categorical variable name via --group-col
• (Optional) Continuous variable for median stratification (e.g., gene expression)

Outputs

• PNG file (default): High-resolution Kaplan-Meier curve with all annotations
• SVG file (if --output-svg): Scalable vector graphics for editing in Illustrator/Inkscape
• survival_stats.tsv: Table with group, n, n_events, median_survival, CI_lower, CI_upper, p_value
• Console output: Summary statistics and test results

Procedure

Step 1: Load and validate data

1. Read CSV/TSV into pandas DataFrame
2. Check for required columns: --time-col, --event-col, --group-col
3. Validate data types: time should be numeric, event should be 0/1
4. Remove rows with missing values in key columns
5. Handle median stratification if --split-by-median is set

Step 2: Kaplan-Meier estimation (per group)

For each group:

1. Sort records by time-to-event
2. Identify unique event times
3. At each event time t, compute:

• d_i = number of events at time t
• n_i = number at risk at time t
• S(t) = S(t-1) × (1 - d_i / n_i) [product of conditional survival]

1. Compute Greenwood's variance:

• Var(S(t)) = S(t)^2 × sum(d_i / (n_i × (n_i - d_i)))

1. Compute 95% CI using log-log transformation:

• α = sqrt(Var(log(-log(S))))
• CI = exp(-exp(log(-log(S)) ± 1.96 × α))

1. Identify median survival time (time at which S(t) = 0.5)

Step 3: Statistical testing

Log-rank test:

1. Compute observed vs. expected events across all event times
2. O_i = observed events in group i at each time
3. E_i = expected events = (d_i × n_i) / N, where N = total at risk
4. Chi-squared statistic: χ² = (O_i - E_i)^2 / E_i, df = n_groups - 1
5. Compute p-value from chi-squared distribution (Wilson-Hilferty normal approx for small sample)

Wilcoxon (Peto-Wilcoxon) test:

1. Weight each comparison by number at risk: w_i = n_i (gives more weight to early events)
2. Otherwise same as log-rank test with weighted statistics

Step 4: Plot generation (matplotlib)

1. Create figure with specified dimensions and DPI
2. For each group, plot step function:

• x = event times, y = S(t)
• Use "where=post" for step function
• Color from palette (Set1, tab10, or custom)
• Linewidth customizable

1. Add shaded confidence interval bands (fill_between with alpha transparency)
2. Add censoring tick marks at censored times (scatter plot with marker="|" or "+")
3. Add vertical dashed lines at median survival times (if --show-median)
4. Add horizontal line at S(t)=0.5 (if --show-median)
5. Add at-risk table below x-axis (ax.text for each time point × group, showing n at risk)
6. Annotate p-value in corner (if --show-pvalue)
7. Customize labels, legend, colors, fonts, axis limits

Step 5: Output generation

1. Save figure to PNG at specified DPI (default 300)
2. Save to SVG if requested
3. Write survival_stats.tsv with summary statistics per group
4. Print summary to console

Key execution patterns

# Basic: Two-group KM curve (control vs. treatment)
python scripts/plot_survival.py \
  --input survival_data.csv \
  --time-col time_months \
  --event-col event \
  --group-col treatment \
  --output survival_plot.png \
  --title "Overall Survival by Treatment Group" \
  --show-pvalue \
  --show-at-risk
 
# Median stratification for gene expression (high vs. low)
python scripts/plot_survival.py \
  --input tcga_data.tsv \
  --time-col os_months \
  --event-col os_event \
  --split-by-median \
  --split-col gene_expression_level \
  --output gene_expr_survival.png \
  --title "Overall Survival by Gene Expression" \
  --show-median \
  --show-ci
 
# Multiple groups with custom colors and log-rank test
python scripts/plot_survival.py \
  --input clinical_trial.csv \
  --time-col time_days \
  --event-col event_status \
  --group-col dose_group \
  --group-order "placebo,low_dose,high_dose" \
  --group-colors "#e41a1c,#377eb8,#4daf4a" \
  --output dose_response_survival.png \
  --test logrank \
  --show-pvalue \
  --time-unit months \
  --fig-width 10 \
  --fig-height 7
 
# Clinical publication-quality figure
python scripts/plot_survival.py \
  --input cancer_cohort.tsv \
  --time-col efs_months \
  --event-col efs_event \
  --group-col biomarker_status \
  --output publication_figure.png \
  --output-svg \
  --title "Event-Free Survival by Biomarker Status" \
  --xlabel "Months from diagnosis" \
  --ylabel "Event-free survival probability" \
  --show-at-risk \
  --show-median \
  --show-ci \
  --show-pvalue \
  --test both \
  --dpi 300 \
  --fig-width 9 \
  --fig-height 6
 
# Compare log-rank and Wilcoxon tests
python scripts/plot_survival.py \
  --input early_stopping_trial.csv \
  --time-col weeks \
  --event-col event \
  --group-col arm \
  --output early_events.png \
  --test both \
  --show-pvalue \
  --pvalue-location top_left
 
# Stratified analysis (multiple strata)
# Create stratified dataset, then run separately:
python scripts/plot_survival.py \
  --input subset_stratum_a.csv \
  --time-col time \
  --event-col event \
  --group-col treatment \
  --output survival_stratum_a.png

Parameter decision guide

Failure modes