R/plot_single_genes.R

In scMAGeCK: Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

# function definitions ##### version: 02-22-2019 should sync from the version in macbook:
# /Users/weili/Dropbox/work/cropseq/Shendure/nmeth18/multiple_guides_function.R

plot_single_genes <- function(targetob, gene1, targetgene, haslog = TRUE, plotfigure = TRUE, ngctrlgene = c("NonTargetingControlGuideForHuman"), 
    indmatrix = NULL) {
    # plot single gene ko effect if indmatrix =NULL, use targetobj@metadata to identify cell groups
    # else, use indmatrix where cells that do not bear gene1 target as controls
    
    if (is.null(indmatrix)) {
        cell_ctrl = rownames(targetob@meta.data)[which(targetob@meta.data$geneID %in% ngctrlgene)]
        cell_gene1 = rownames(targetob@meta.data)[which(targetob@meta.data$geneID == gene1)]
        if (length(cell_gene1) == 0) {
            gene1 = sub("-", "_", gene1)
            cell_gene1 = rownames(targetob@meta.data)[which(targetob@meta.data$geneID == gene1)]
        }
    } else {
        cell_ctrl = rownames(indmatrix)[indmatrix[, gene1] == FALSE]
        cell_gene1 = rownames(indmatrix)[indmatrix[, gene1] == TRUE]
    }
    # cell_gene2=rownames(targetob@meta.data)[which(targetob@meta.data$geneID==gene2)]
    # mg_geneid=paste(gene1,gene2,sep='_') cell_merged=select_pair_genes[[mg_geneid]]
    scalef = getscaledata(targetobj)
    t_exp = scalef[targetgene, c(cell_ctrl, cell_gene1)]
    if (min(t_exp) < 0) {
        t_exp = t_exp - (min(t_exp)) + 0.1
    }
    t_type = c(rep("NegCtrl", length(cell_ctrl)), rep(gene1, length(cell_gene1)))
    t_type = factor(t_type, levels = c("NegCtrl", gene1))
    ds = data.frame(Expression = t_exp, Type = t_type, Cells = c(cell_ctrl, cell_gene1))
    
    if (plotfigure) {
        p <- ggplot(ds, aes(x = Type, y = Expression)) + geom_violin() + geom_point(position = position_jitter(w = 0.1, 
            h = 0)) + ggtitle(paste(targetgene, "expression"))
        if (haslog) {
            p = p + scale_y_log10()
        }
        # ggtitle(paste(ensemblID,geneID))
        message(p)
    }
    
    return(ds)
}
TRUE