.pl
The proteopy.pl module provides publication-ready visualizations for quality
control, exploratory analysis, and statistical results.
Intensity Distributions
Plot peptide intensities across samples for the requested proteins. |
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Plot peptide intensities across samples for the requested proteins. |
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Plot histogram(s) of var intensities, optionally colored by imputation status. |
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Plot intensity distributions as boxplots, either per observation or pooled by a categorical grouping. |
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Boxplot of intensities for one or more variables. |
Quality Control
Plot variable intensities vs their abundance rank. |
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Plot a binary detection heatmap of intensities across samples and features. |
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Plot a histogram of completeness across observations or variables. |
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Plot a histogram of completeness per sample (observation). |
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Plot a histogram of completeness per variable. |
Metadata exploration
Plot sample (obs) counts per category (optionally stratified). |
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Plot the number of detected peptides per observation. |
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Plot the number of detected proteins per observation. |
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Plot the distribution of the number of first-category entries per second category. |
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Plot the distribution of the number of first-category entries per second category. |
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Plot the distribution of the number of first-category entries per second category. |
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Compute per-group coefficients of variation and plot their distributions. |
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Plot a clustered correlation heatmap across samples (obs). |
Proteoform Inference
Scatter plot of COPF proteoform scores vs. p-values. |
Differential Analysis
Visualize differential abundance results as a volcano plot. |
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Display boxplots of intensities for top differentially abundant variables. |
Clustering
Plot a clustered heatmap of variable profiles across samples or groups. |
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Plot silhouette scores for hierarchical clustering. |
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Plot within-cluster sum of squares (elbow plot) for hierarchical clustering. |
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Plot cluster profile intensities across observations. |