analysis.py 文件源码

def inspect_bulk(df, df_bulk, de_genes, de_genes_bulk):
    """
    """
    quant_types = [("bitseq", df_bulk)]

    for quant_type, exp_matrix in quant_types:
        print(quant_type)

        # Boxplots of expression
        fig, axis = plt.subplots(1)
        sns.boxplot(data=pd.melt(exp_matrix), x="grna", y="value", hue="condition", ax=axis)
        fig.savefig(os.path.join("results", "bulk", "bulk_samples.qc.{}.expression_boxplots.png".format(quant_type)), dpi=300, bbox_inches="tight")

        # Heatmap and correlation on signature genes
        # derived from bulk
        # derived from scRNA
        for geneset in ["de_genes", "de_genes_bulk"]:
            g = sns.clustermap(
                exp_matrix.ix[eval(geneset)].dropna(),
                z_score=0,
                row_cluster=True, col_cluster=True,
                xticklabels=True, yticklabels=True,
                figsize=(15, 15))
            for item in g.ax_heatmap.get_yticklabels():
                item.set_rotation(0)
            for item in g.ax_heatmap.get_xticklabels():
                item.set_rotation(90)
            g.fig.savefig(os.path.join("results", "bulk", "bulk_samples.qc.{}.{}.png".format(quant_type, geneset)), dpi=300, bbox_inches="tight")

            g = sns.clustermap(
                exp_matrix.ix[eval(geneset)].dropna().corr(),
                row_cluster=True, col_cluster=True,
                xticklabels=True, yticklabels=True,
                figsize=(15, 15))
            for item in g.ax_heatmap.get_yticklabels():
                item.set_rotation(0)
            for item in g.ax_heatmap.get_xticklabels():
                item.set_rotation(90)
            g.fig.savefig(os.path.join("results", "bulk", "bulk_samples.qc.{}.{}.correlation.png".format(quant_type, geneset)), dpi=300, bbox_inches="tight")