occdn.limour.top/source/_posts/cellphonedb：筛选细胞和通路.md

---

title: cellphoneDB：筛选细胞和通路 tags: [] id: '1728' categories:

• - 生信

• • 细胞通讯

    date: 2022-04-25 17:47:05

    f_cpdb_select_pathway <- function(lc_res, grep_i_p_list=NULL){
    if(is.null(grep_i_p_list)){
    grep_i_p_list = list(
        chemokines = "^CXCCCLCCRCX3XCLXCR",
        th1 = "IL2IL12IL18IL27IFNGIL10TNF$TNF LTALTBSTAT1CCR5CXCR3IL12RB1IFNGR1TBX21STAT4",
        th2 = "IL4IL5IL25IL10IL13AREGSTAT6GATA3IL4R",
        th17 = "IL21IL22IL24IL26IL17AIL17AIL17FIL17RAIL10RORCRORASTAT3CCR4CCR6IL23RATGFB",
        treg = "IL35IL10FOXP3IL2RATGFB",
        costimulatory = "CD86CD80CD48LILRB2LILRB4TNFCD2ICAMSLAMLT[AB]NECTIN2CD40CD70CD27CD28CD58TSLPPVRCD44CD55CD[1-9]",
        coinhibitory = "SIRPCD47ICOSTIGITCTLA4PDCD1CD274LAG3HAVCRVSIR",
        niche = "CSF"
    )
    }
    lc_res$grep_i_p_list = list()
    for(name in names(grep_i_p_list)){
    lc_res$grep_i_p_list[[name]] = unique(grep(grep_i_p_list[[name]], lc_res$s_m_p$interacting_pair,value = T))
    }
    lc_res
    }
    

    f_cpdb_select_cluster <- function(lc_res, grep_celltype){
    lc_res$grep_celltype <- unique(grep(grep_celltype, lc_res$s_m_p$celltype, value = T))
    lc_res
    }
    

    f_cpdb <- function(lc_res){
    res <- lc_res$s_m_p
    if(!is.null(lc_res$grep_i_p_list)){
            
    res <- res %>% dplyr::filter(interacting_pair %in% reduce(lc_res$grep_i_p_list, c))
    }
    if(!is.null(lc_res$grep_celltype)){
    res <- res %>% dplyr::filter(celltype %in% lc_res$grep_celltype)
    }
    res
    }
    

示例

sce <- f_readcellphoneDB('crpc_strom_epi_new')
sce <- f_cpdb_select_cluster(sce, 'iCAF')
grep_i_p_list = list(
    vegf = "VEGFFGFIGF" 
)
sce <- f_cpdb_select_pathway(sce, grep_i_p_list)
f_cDB_dotplot(f_cpdb(sce))