R/plot_gi_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_gi_genes <- function(targetobj, gene1, gene2, targetgene, select_pair_genes, haslog = TRUE, plotfigure = TRUE, 
    ngctrlgene = c("NonTargetingControlGuideForHuman")) {
    if (gene1 > gene2) {
        tx = gene2
        gene2 = gene1
        gene1 = tx
    }
    cell_ctrl = rownames(targetobj@meta.data)[which(targetobj@meta.data$geneID %in% ngctrlgene)]
    cell_gene1 = rownames(targetobj@meta.data)[which(targetobj@meta.data$geneID == gene1)]
    cell_gene2 = rownames(targetobj@meta.data)[which(targetobj@meta.data$geneID == gene2)]
    mg_geneid = paste(gene1, gene2, sep = "_")
    cell_merged = select_pair_genes[[mg_geneid]]
    cell_merged = cell_merged[cell_merged %in% rownames(targetobj@meta.data)]
    
    # browser()
    
    scalef = getscaledata(targetobj)
    t_exp = scalef[targetgene, c(cell_ctrl, cell_gene1, cell_gene2, cell_merged)]
    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)), rep(gene2, length(cell_gene2)), 
        rep(mg_geneid, length(cell_merged)))
    t_type = factor(t_type, levels = c("NegCtrl", gene1, gene2, mg_geneid))
    ds = data.frame(Expression = t_exp, Type = t_type, Cells = c(cell_ctrl, cell_gene1, cell_gene2, 
        cell_merged))
    
    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