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CellDiff Installation Guide

Package Ready for Installation

The CellDiff package has been cleaned and prepared for installation. All temporary files, test scripts, and debug code have been removed.

Quick Installation

From GitHub

# Install devtools if not already installed
if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")

# Install CellDiff from GitHub
devtools::install_github("guokai8/CellDiff")

From Local Source

# If you have the source code locally
devtools::install("path/to/CellDiff")

# Or from the built tar.gz file
install.packages("path/to/CellDiff_0.1.3.tar.gz", repos = NULL, type = "source")

What Was Fixed

1. Core Function Improvements

  • heatDiffM: Fixed return statement to display correctly in RStudio

    • Changed from invisible(final_heatmap) to return(final_heatmap)
    • Fixed custom_pairs index conversion bug
    • Fixed width/height swap in big_heatmap mode
    • Fixed legend breaks for edge cases

  • heatDiff: Fixed missing scPalette function

    • Replaced with assignColors() from utils.R

  • rankDiffM: Fixed custom_pairs index conversion

  • ContriDiffM: Added custom_pairs comparison method support

  • scatterDiff2DM: Fixed custom_pairs index conversion and quadrant label positioning

2. Files Removed

All temporary test, debug, and documentation files have been removed:

  • Test scripts (test_.R, debug_.R, etc.)
  • Temporary documentation (CHEAT_SHEET.txt, COMPLETE_GUIDE.md, etc.)
  • Test PDF outputs
  • Test data files (cellchat_objects_list.rds)

3. Files Kept

Essential package files:

  • R/ - All core function files (fixed and working)
  • man/ - Documentation files
  • data/ - Package data (cellchatlist.rda)
  • vignettes/ - Package vignettes
  • DESCRIPTION - Package metadata
  • NAMESPACE - Exported functions
  • README.md - Updated with custom_pairs examples
  • LICENSE - GPL-3 license

Using the Fixed Functions

Basic Usage

library(CellDiff)

# Load your CellChat objects
cellchat_list <- list(WT = cellchat_wt, KO = cellchat_ko, DKO = cellchat_dko)

# The functions now work correctly in RStudio
heatDiffM(
  object.list = cellchat_list,
  comparison_method = "custom_pairs",
  custom_comparisons = list(
    c("WT", "KO"),
    c("KO", "DKO"),
    c("WT", "DKO")
  ),
  measure = "sender",
  use_log2fc = TRUE,
  show_values = TRUE,
  big_heatmap = TRUE,
  color.heatmap = c("blue", "white", "red")
)

Comparison Methods

The multi-condition functions now support three comparison methods:

  1. all_vs_ref: Compare all conditions to a reference

    heatDiffM(object.list, comparison_method = "all_vs_ref", reference = "WT")

  2. all_vs_all: All pairwise comparisons

    heatDiffM(object.list, comparison_method = "all_vs_all")

  3. custom_pairs: Specific comparison pairs (NEW - FIXED!)

    heatDiffM(
  object.list,
  comparison_method = "custom_pairs",
  custom_comparisons = list(c("WT", "KO"), c("KO", "DKO"))
)

Optional Helper Functions

The package includes optional helper functions for advanced use cases:

  • view_heatmap() - View heatmaps via PNG rendering (useful for very complex plots)
  • save_heatmap() - Save heatmaps to PDF safely

These are not exported by default but are available in R/view_heatmap.R and R/save_heatmap.R if needed.

Verification

To verify the installation:

library(CellDiff)

# Check that functions are available
ls("package:CellDiff")

# Test with example data
data(celllist)
heatDiff(object.list = celllist, comparison = c(1, 2), measure = "sender")

Support

For issues or questions:

Version Information

Current Version: 0.1.3 Date: 2025-05-02 Built Package: CellDiff_0.1.3.tar.gz (23MB)