build-heatmaps-imp2
Build heatmaps of cell frequencies and maker intensities for correct interpretations
Overview
This repository accompanies the article entitled “Build heatmaps of cell frequencies and maker intensities for correct interpretations” from E. Lohmann, L. Gorvel and S. Granjeaud, and submitted to “Immunophenotyping: Methods and Protocols, Second Edition” edited by Angélique Biancotto and Pradeep K. Dagur in the book series “Methods in Molecular Biology”. The preprint is available at bioRXiv.
The aim is to understand the steps for building heatmaps of frequencies. Data files to start to follow the protocols are here. Data originates from the study of Michlmayr et al.. They performed a 37-plex mass cytometry acquisition of peripheral blood mononuclear cells (PBMCs) of acute- and convalescent-phase samples obtained from 43 children naturally infected with chikungunya virus. Their analysis classified cells into 57 sub-communities of canonical leukocyte phenotypes and revealed a monocyte-driven response to acute infection, with the greatest expansions in “intermediate” CD14++CD16+ monocytes and an activated subpopulation of CD14+ monocytes. The FCS files and the attachments files are available on FlowRepository under id FR-FCM-Z238. We focused on the smallest subset of cell populations called “Assignment”.
Data files
- output data files to start the protocols
- input files for 01_extract_from_fcs_to_db
- extract results from 01_extract_from_fcs_to_db
R scripts and reports
Extensive R scripts are available below as well as the preparation script.
- 04_counts_to_heatmap Rmd
- 03_mfis_to_heatmap Rmd
- 02_prepare_from_extraction Rmd
- 01_extract_from_fcs_to_db Rmd
Contact
Contact us by mail or open an issue on the repository.