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ggpicrust2 2.3.2

Bug Fixes

• Fixed MetaCyc pathway annotation NA description issue (#154):
  • Standardized MetaCyc reference data column names from ‘X1’/‘X2’ to ‘id’/‘description’
  • Applied fix in all three loading paths of load_reference_data function
  • Resolves column name mismatch that caused all MetaCyc annotations to return NA
  • Tested with 100% success rate on sample data
  • Maintains backward compatibility with KO and EC pathway types

ggpicrust2 2.3.1

Bug Fixes

• Fixed MetaCyc reference data loading issue:
  • Enhanced the file search mechanism in the load_reference_data function
  • Added multiple search paths for reference data files
  • Improved error messages with more diagnostic information
  • Fixed “Reference data file not found” error that some users encountered

ggpicrust2 2.3.0

Bug Fixes

• Fixed NA handling in pathway_errorbar function:
  • Improved handling of NA values in the feature column
  • Added robust error checking for group ordering option
  • Prevents errors when processing MetaCyc pathway data with missing annotations
• Enhanced pathway_pca function to handle zero variance data:
  • Automatically detects and filters out columns (samples) with zero variance
  • Automatically detects and filters out rows (pathways) with zero variance
  • Updates metadata to match remaining samples after filtering
  • Provides informative warnings about removed samples/pathways
  • Improves error handling with clear diagnostic messages
• Fixed file extension handling in ko2kegg_abundance function:
  • Resolved “the condition has length > 1” error when processing files
  • Improved extension detection for different file types
  • Enhanced robustness for handling various input formats

ggpicrust2 2.2.2

Bug Fixes

• Fixed column name compatibility issues in reference data files:
  • Standardized column names in KO_reference.RData and EC_reference.RData
  • Resolved warnings when using pathway_annotation() with ko_to_kegg=FALSE
  • Improved backward compatibility with existing code

ggpicrust2 2.2.1

Bug Fixes

• Added aggregate_by_group parameter to pathway_heatmap function:
  • Allows displaying representative samples (e.g., mean) for each group instead of all individual samples
  • Improved handling of NA values in heatmap visualization
  • Added aggregate_fun parameter for customizing the aggregation function

ggpicrust2 2.1.4

Reference Data Updates

• Updated reference databases for improved pathway annotation:
  • EC reference data updated from 3,180 to 8,371 entries (163% increase)
  • KO reference data updated from 23,917 to 27,531 unique KO IDs (15.4% increase)
  • These updates provide more comprehensive and accurate pathway annotations

ggpicrust2 2.1.1

Bug Fixes

• Improved error handling for KEGG database connections (Issue #138):
  • Added robust error handling for HTTP 404 errors when connecting to the KEGG database
  • Function now continues processing other KO IDs even when some IDs return HTTP 404 errors
  • Added detailed logging about which KO IDs were not found
  • Only throws a fatal error when all KO IDs fail to be processed
  • Includes summary statistics about successful, not found, and error counts
• Fixed the LinDA analysis for multi-group comparisons (Issue #144):
  • Modified the perform_linda_analysis function to handle multi-group comparisons correctly
  • The function now creates separate result entries for each pairwise comparison
  • Added the log2FoldChange column to the results for effect size information

ggpicrust2 2.1.0

Major Changes

• Added Gene Set Enrichment Analysis (GSEA) functionality with the following new functions:

  • pathway_gsea(): Performs GSEA analysis, supporting KEGG, MetaCyc, and GO pathways
  • visualize_gsea(): Creates visualizations of GSEA results, including enrichment plots, dotplots, barplots, network plots, and heatmaps
  • compare_gsea_daa(): Compares GSEA and Differential Abundance Analysis (DAA) results
  • gsea_pathway_annotation(): Adds pathway annotations to GSEA results
  • ggpicrust2_extended(): Provides integrated analysis combining ggpicrust2 and GSEA functionality

• Improved network and heatmap visualization capabilities with richer parameter options and better error handling

• Added preliminary support for MetaCyc and GO pathways

• Fixed various bugs and optimized code structure

ggpicrust2 2.0.1

Major Changes

• Fixed a bug in the pathway_annotation function, resolving issues caused by changes in the KEGG API response structure

ggpicrust2 2.0.0

主要变更

• Refactored the package dependencies, moving most Bioconductor packages from Imports to Suggests, reducing mandatory dependencies.

• Added conditional checks to ensure that packages are only used when they are available.

• Fixed the function export issue, ensuring that all public API functions are correctly exported.

• Updated the example code, improving its stability and compatibility.

• Updated the documentation format to comply with the latest CRAN standards.

• Fixed invalid URL links in the README.

• Optimized code quality, removing unused variables.

• Added missing import declarations to ensure package integrity.

ggpicrust2 1.7.5

ggpicrust2 1.7.2

ggpicrust2 1.7.1

ggpicrust2 1.7.0

ggpicrust2 1.6.6

ggpicrust2 1.6.5

ggpicrust2 1.6.4

ggpicrust2 1.6.3

ggpicrust2 1.6.2

ggpicrust2 1.6.1

ggpicrust2 1.6.0

ggpicrust2 1.5.1

ggpicrust2 1.5.0

ggpicrust2 1.4.12

ggpicrust2 1.4.11

ggpicrust2 1.4.10

ggpicrust2 1.4.9

ggpicrust2 1.4.8

ggpicrust2 1.4.7

ggpicrust2 1.4.6

ggpicrust2 1.4.5

ggpicrust2 1.4.4

ggpicrust2 1.4.3

ggpicrust2 1.4.2

ggpicrust2 1.4.1

ggpicrust2 1.4.0

ggpicrust2 1.3.1

ggpicrust2 1.3.0

ggpicrust2 1.2.3

ggpicrust2 1.2.2

ggpicrust2 1.2.1

ggpicrust2 1.2.0

ggpicrust2 1.1.1

ggpicrust2 1.1.0

ggpicrust2 1.0.1

ggpicrust2 1.0.0

ggpicrust2 0.2.0

• Added a NEWS.md file to track changes to the package.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.