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Available Documentation

  • pyoncoplot Documentation
    • Start Here
    • Minimal Example
    • Documentation Map
      • Installation
        • Development Install
        • Runtime Dependencies
        • Verify The Install
        • Next Step
      • Quickstart
        • Input Data
        • Interactive Plotly Plot
        • Static Matplotlib Plot
        • Result Object
        • Where To Go Next
      • Data Inputs
        • Required Columns
        • Example Mutation Table
        • Multi-Hit Behavior
        • Gene Selection
        • Sample Selection
        • Row and Sample Filters
        • Validation Rules
      • API Reference
        • oncoplot
        • merge_oncoplot_params
        • OncoplotResult
        • prepare_oncoplot_data
        • identify_top_genes
        • score_sample_by_gene_rank
        • rank_genes_by_pathway
        • prettify
        • Palette Helpers
      • Options Reference
        • Size and Layout
        • Labels and Axes
        • Legends
        • Tile Styling
        • Fonts
        • Titles
        • TMB and Gene Bar
        • Pathways
        • Metadata
        • Text Prettification
        • Common Bundles
      • Palettes
        • Mutation Palette
        • Metadata Palette
        • Variant Value Palette
        • TMB Palette
        • Default Palettes
        • Practical Color Guidance
      • Metadata and TMB
        • Metadata Table Schema
        • Metadata Columns in Mutation Data
        • Metadata Filtering
        • Numeric Metadata
        • Categorical Metadata Order
        • TMB Inference
        • Custom TMB Data
      • Pathways and Sorting
        • Default Gene Ranking
        • Explicit Gene Order
        • Pathway Input
        • Sample Ordering
        • Metadata Sorting
        • Showing All Samples
      • Rendering Backends
        • Plotly
        • Matplotlib
        • Choosing A Backend
        • Backend Support Matrix
      • Example Gallery
        • Render The Clean Gallery
        • Regenerate Gallery Inputs
        • BRCA Comparison Sheets
        • Accepted Clean Baselines
        • Presets
        • Config-Driven Runs
        • Input Families
        • Related Examples
      • Example Plot Source Citations
        • Plot-To-Source Map
        • Directly Used Papers
        • TCGA And Xena Data Sources
        • Documentation And Source Image Pages
        • Notes
      • Basic Example
      • Metadata Example
      • BRCA Gallery Example
        • Render The Default BRCA Outputs
        • Render Comparison Sheets
        • Inputs
        • Inspect The Preset Code
      • Migration From ggoncoplot
        • Argument Mapping
        • Options Mapping
        • R-Style Concept
        • Python Version
        • Important Differences
        • ggoncoplot Parity Status
        • Recommended Migration Path
      • Development
        • Local Setup
        • Repository Layout
        • Regenerate Gallery Inputs
        • Regenerate Gallery Images
        • Adding A Gallery Preset
        • Documentation Changes
      • Troubleshooting
        • Missing Column Errors
        • Empty Or Missing Sample/Gene Identifiers
        • Palette Coverage Errors
        • Metadata Duplicate Sample Errors
        • Samples Disappear
        • Plotly Image Export Fails
        • Matplotlib Font Warnings
        • Very Large Cohorts
  • adata_science_tools docs
    • Available pages
    • Notes
      • _IO
        • save_dataset
        • make_df_obs_adataX
        • Data source selection
        • Column labeling
        • Row indexing
        • include_obs
        • Dense conversion and scale
        • Current limitations and caveats
      • _column_plots
        • Public entry points
        • Shared data model
        • barh_column
        • l2fc_dotplot_single
        • l2fc_dotplot_column
        • barh_l2fc_dotplot_column
        • Advanced composite variants
        • Common caveats
      • _corr_dotplots
        • Main entry points
        • corr_dotplot
        • corr_dotplot_dev
        • spearman_cor_dotplot
        • Secondary helpers
        • Example with plain DataFrame
      • _datapoints
        • datapoints
      • _diff_test
        • Full signature
        • Supported test families
        • Input modes
        • Required keys and pairing rules
        • Examples by workflow
        • Output table shape
        • Save and storage behavior
        • Validation and edge cases
        • Practical notes
      • _expectation_based_covar_correction
        • Core model
        • calculate_expectations
        • Expectation table schema
        • model_spec
        • Saving and reloading artifacts
        • predict_expectation
        • regress_out
        • excess_expectation
        • convert_ols_summary_to_expectation_df
        • reconstruct_expectation_model_spec
        • Wrapper workflow
        • Common validation errors
        • Practical workflow summary
      • _histograms
        • Main entry point
        • adata_histograms
        • Full signature
        • Basic example
        • Legend positioning
        • Supported input modes
        • All-variable stacked histogram
        • Variable-grouped histograms
        • Filtering and Subsets
        • Important behavior
      • _metab_IO
        • Full signature
        • Basic parsing workflow
        • Layer creation
        • Returned AnnData
        • Save behavior
        • External metadata merge
        • Example with external metadata
        • Current implementation caveats
        • When to use this module
      • _model_fit
        • OLS workflow
        • MixedLM workflow
        • Filtering before fit
        • Low-level *_wide(...) APIs
        • Result table schema
        • Sidecar YAML model specs
        • adata.uns storage
        • Behavior and constraints
        • Feature annotation merge
        • Practical guidance
      • _paired_datapoints
        • Main entry point
        • paired_datapoints
        • Full signature
        • Basic AnnData example
        • Title and axis label placement
        • Synthetic example plot
        • Supported input modes
        • Pairing behavior
        • Bounds
        • ref_vs_target_adata() source values
        • Filtering and subsets
        • Variable grouping and collapse
        • Logging
        • Return value
      • _plots
        • volcano_plot_generic
        • qqplot
        • timeseries_paired_datapoints
        • Coverage note
      • _plots_depreciated
        • Legacy entry points
        • Preferred replacements
        • Important differences from the modern APIs
        • Recommendation
        • Coverage note
      • _preprocessing
        • Main row-operation entry points
        • ref_vs_target_adata
      • _row_plots
        • plot_columns
        • Coverage note
      • _simulate_data
        • Main entry points
        • sim_observations_covars
        • sim_covar_dependent_features
        • sim_covar_dependent_dataset
        • Repo example workflow
      • _somascan_IO
        • read_adat_2_AnnData
        • soma_fill_sampletype_obs_values
        • soma_make_adata_index_unique_by_merge
        • make_df_obs_adataX_soma
        • Practical guidance
        • Current caveats
      • _utils
        • Public entry points
        • show_tol_colors
        • show_colors
        • Coverage note
      • _venn_plots
        • Public functions
        • venn_plot_2list
        • venn_plot_3list
        • geneset_enrichment_venn
        • geneset_enrichemnt_ol_ven_M_n_N_x
        • Coverage note
      • palettes
        • Main palette constants
        • Typical usage
        • Internal helper
        • Coverage note
  • single_cell_python_tools docs
    • Documentation Pages
    • Source Links
      • Installation
        • Conda Environment
        • Editable Install
        • Verify Import
      • Quickstart
        • Notebook Path Setup
        • Function-Based Workflow
        • DATASET_class Workflow
      • DATASET_class
        • Constructor
        • Data And Output Methods
        • QC And Filtering Methods
        • Transform Methods
        • Clustering Methods
        • Plotting Methods
        • Notes
      • Preprocessing IO
        • reset_cellxgene_var_names
        • downcast_layers_to_float32
      • Preprocessing QC
        • annotate_QC_genes
        • calculate_qc_metrics
        • plot_QC_metrics_scatter
        • plot_QC_metrics_violin
        • plot_qc_metrics
        • annotate_n_view_adata_raw_counts
        • basic_filitering
        • filter_cells_by_anotated_QC_gene
        • remove_genes
      • Preprocessing Transform Data
        • process2scaledPCA
        • norm_log
        • HVG_selection_log_norm_seurat
        • HVG_selection_log_norm_seurat_v3
        • HVG_removal
        • regress_out_anotated_QC_genes
        • scale_func
        • PCA_func
        • calc_cell_cycle_score
        • regress_cell_cycle_score_func
      • Preprocessing Clustering
        • leiden_clustering
        • rename_leiden_clusters
        • Legacy Rename Helpers
        • leiden_cluster_sil_score
        • silhouette_walk_Largest_drop
        • silhouette_walk_4_Largest_drops
      • Plotting
        • silhouette_score_n_plot
        • silhouette_score_of_obs_key_n_plot
        • plot_batch_obs_key_of_obs_key2
        • plot_adata_row_total_dist
        • plot_adata_raw_and_X_rowdist_old
        • plot_adata_raw_and_X_rowdist
      • Deprecated Plotting Helpers
        • plot_batch_obs_key_of_obs_key2_old
        • plot_percent_obs_key2_per_batch_obs_key
      • Scanpy Tools
        • General Utilities
        • Annotation Helpers
        • Differential Expression And Enrichment
        • Filtering And Summaries
        • Notes
      • Ingest Verbose
        • ingest_verbose
        • Ingest
        • Export Note
      • Example Notebooks
        • PBMC3k
        • Publishing Policy
      • API Reference
        • Top-Level Namespace
        • DATASET_class
        • sctl.pp
        • sctl.pl
        • sctl.tl
        • Direct Module APIs
      • Development
        • Repository Layout
        • Documentation Maintenance
        • Public API Notes
      • Troubleshooting
        • Import Fails With Missing Scanpy
        • Python Version Mismatch
        • Notebook Cannot Find The Package
        • Output Directories Are Missing
        • Links In Published Docs Go To GitHub
  • Coding Cheatsheets
    • Documentation
    • Full Cheatsheets
    • Fast Project Startup
    • GitHub and Git
      • Clone, Status, and History
      • Stage, Commit, and Push
      • Branches, Remotes, and Pull Requests
      • Submodules
    • Conda Environments
      • Setup and Channels
      • Create, Use, and Remove Environments
      • Packages, Environment Files, and Jupyter
    • Bash
      • Navigation and Files
      • View, Search, and Redirect
      • Permissions, Environment, and Processes
    • Python
      • Run Python and Manage Packages
      • Script Pattern, Paths, and Files
      • Arguments, Testing, and Debugging
    • R
      • Run R and Manage Packages
      • Files and Data Frames
      • dplyr, ggplot2, and Jupyter
    • SQL and PostgreSQL
      • Connect and Navigate
      • Query Data
      • Join, Group, and Modify
      • Import, Export, and Back Up
    • Legacy Material
      • GitHub and Git Cheatsheet
        • Repository Setup
        • Status and History
        • Stage, Commit, and Push
        • Pull and Sync
        • Submodules
        • Branches
        • Merge Basics
        • Undo Common Mistakes
        • GitHub CLI
      • Conda Environments Cheatsheet
        • Setup
        • Create and Activate
        • Install and Update Packages
        • Environment Files
        • Jupyter Kernels
        • Clean Up
      • Bash Cheatsheet
        • Navigation
        • Files and Directories
        • View Files
        • Search
        • Pipes and Redirects
        • Permissions
        • Environment and History
        • Processes
      • Python Cheatsheet
        • Run Python
        • Virtual Environments and Packages
        • Basic Script Pattern
        • Imports and Paths
        • File I/O
        • Lists and Dictionaries
        • Functions and Errors
        • Command Line Arguments
        • Debugging
      • R Cheatsheet
        • Run R
        • Packages
        • Working Directory and Files
        • Vectors, Lists, and Factors
        • Data Frames
        • dplyr
        • Plotting
        • Jupyter and RStudio
      • SQL and PostgreSQL Cheatsheet
        • Connect with psql
        • psql Navigation
        • Databases and Tables
        • Select and Filter
        • Joins and Grouping
        • Insert, Update, and Delete
        • CSV Import and Export
        • Backup and Restore
        • Admin
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