How to interpret the HTML report generated by cellCellReport function
29 October 2024
Package
scTensor 2.17.0
Contents
- 1 Introduction
- 2 Interpretation of “1. About scTensor Algorithm”
- 3 Interpretation of “2. Global statistics and plots”
- 4 Interpretation of “3. Ligand-Cell Patterns”
- 5 Interpretation of “4. Receptor-Cell Patterns”
- 6 Interpretation of “5. CCI-wise Hypergraph”
- 7 Interpretation of “6. Gene-wise Hypergraph”
- 8 Interpretation of “7. (Ligand-Cell, Receptor-Cell, LR-pair) Patterns”
- Session information
1 Introduction
Here, we explain the way to interpret of HTML report generated by cellCellReport.
If cellCellDecomp is properly finished, we can perform cellCellReport
function to output the HTML report.
The results can be confirmed by typing example(cellCellReport).
The report will be generated in the temporary directory (it costs 5 to 10 minutes).
The output directory contains some files and directories as follows.
- index.{Rmd,html} : The main HTML report
- reanalysis.RData : The R binary file for using in the HTML report and reanalysis of scTensor
- Workflow_2.png : The figure for the section 1. About scTensor Algorithm in the HTML report
- figures : The directory containing some figures for the HTML report
- ligand.{Rmd,html} : The HTML report for the section 6. Gene-wise Hypergraph in the HTML report
- ligand_all.{Rmd,html} : The HTML report for the section 6. Gene-wise Hypergraph in the HTML report
- receptor.{Rmd,html} : The HTML report for the section 6. Gene-wise Hypergraph in the HTML report
- receptor_all.{Rmd,html} : The HTML report for the section 6. Gene-wise Hypergraph in the HTML report
- pattern_X_Y.{Rmd,html} : The HTML report for For the section 7. (Ligand-Cell, Receptor-Cell, ) -related L-R Pairs in the HTML report
Here, look at the index.html.
Figure1 : HTML report of
cellCellReport2 Interpretation of “1. About scTensor Algorithm”
In the HTML report, the 1st item describes the overview of scTensor and other CCI-related packages.