screen_dynamics.py 文件源码

def gRNA_swarmplot(s1, s2, prefix=""):
    # Rank of gRNA change
    fig, axis = plt.subplots(3, 2, sharex=True, sharey=True, figsize=(8, 8))
    axis = axis.flatten()

    for i, screen in enumerate(s2.columns[::-1]):
        s = s1.join(s2)  # .fillna(0)
        s = s.iloc[np.random.permutation(len(s))]

        if ("TCR" in screen) or ("Jurkat" in screen) or ("stimulated" in screen) or ("unstimulated" in screen):
            s = s.ix[s.index[~s.index.str.contains("Wnt")]]
            if prefix.startswith("mid_screen-"):
                b = s["gDNA_Jurkat"]
            else:
                b = s["plasmid_pool_TCR"]
            x = s.ix[s.index[s.index.str.contains("Tcr")]]
            y = s.ix[s.index[s.index.str.contains("Essential")]]
            z = s.ix[s.index[s.index.str.contains("CTRL")]]
            b_x = b.ix[s.index[s.index.str.contains("Tcr")]]
            b_y = b.ix[s.index[s.index.str.contains("Essential")]]
            b_z = b.ix[s.index[s.index.str.contains("CTRL")]]
        elif ("WNT" in screen) or ("HEK" in screen):
            s = s.ix[s.index[~s.index.str.contains("Tcr")]]
            if prefix.startswith("mid_screen-"):
                if "_4_" in prefix:
                    b = s["gDNA_HEKclone4"]
                else:
                    b = s["gDNA_HEKclone6"]
            else:
                b = s["plasmid_pool_WNT"]
            x = s.ix[s.index[s.index.str.contains("Wnt")]]
            y = s.ix[s.index[s.index.str.contains("Essential")]]
            z = s.ix[s.index[s.index.str.contains("CTRL")]]
            b_x = b.ix[s.index[s.index.str.contains("Wnt")]]
            b_y = b.ix[s.index[s.index.str.contains("Essential")]]
            b_z = b.ix[s.index[s.index.str.contains("CTRL")]]

        fc_x = np.log2(1 + x[screen]) - np.log2(1 + b_x)
        fc_y = np.log2(1 + y[screen]) - np.log2(1 + b_y)
        fc_z = np.log2(1 + z[screen]) - np.log2(1 + b_z)

        fc_x.name = screen
        fc_y.name = "Essential"
        fc_z.name = "CTRL"

        sns.violinplot(x="variable", y="value", alpha=0.1, inner="box", data=pd.melt(pd.DataFrame([fc_x, fc_y, fc_z]).T), ax=axis[i])
        sns.swarmplot(x="variable", y="value", alpha=0.5, data=pd.melt(pd.DataFrame([fc_x, fc_y, fc_z]).T), ax=axis[i])
        axis[i].axhline(y=0, color='black', linestyle='--', lw=0.5)

        axis[i].set_title(screen)
    sns.despine(fig)
    fig.savefig(os.path.join(results_dir, "gRNA_counts.norm.{}.violin_swarmplot.svg".format(prefix)), bbox_inches="tight")