To illustrate the immune cell atlas and functional heterogeneity of T cell repertoire in murine heart transplantation,we established the murine heterotopic heart transplantation model and isolated CD45 positive cells from cardiac grafts and spleens for single cell transcriptome and TCR sequencing. This repository contains the code used to analyze single-cell RNA-seq with TCR-seq data,bulk RNA-seq data,TCR-seq data. The scRNA+TCR-seq data are available in Gene Expression Omnibus database under the accession number GSE179197 and GSE249989. The RNA-seq data under GSE216869. The TCR-seq data have been deposited into GSE217002.These works reveal immune cell atlas and functional heterogeneity of T cell repertoire in murine heart transplantation. The R scripts are numbered based on function the analyses relate to.