synplot.py 文件源码

def plot_synteny(seq1, ind1, seq2, ind2, y1, y2,
                 featType, matrix, cm, seqname):
    """This function plots all the lines for each"""
    myPatches = []
    colormap = {"COX1": '#c0d9ef',
                   "L": '#e8f1df',
                   "I": '#f7dedc',
                 "16S": '#ff2e00',
                 "12S": '#ffc239',
                 "cal": '#ffff54',
                "COX2": "#7fce66",
                 "ND2": "#00ae60",
                "COX3": "#00aeec",
                 "ND1": "#006fbb",
                   "*": "#ffffff",
                   "(": "#ded9c5",
                   "Q": "#ffc294",
                   "?": "#b5a2c4",
                 "ND4": "#968b5a",
                 "ND3": "#00fc65",
                "ND4L": "#00dcf0",
                 "ND6": "#ff994e",
                 "ND5": "#dc31e6",
                   "X": "#d8d8d8",
                   "G": "#abdce7",
                "CYTB": "#ff0059"}

    for i in range(len(seq1)):
        feat1 = seq1[i]
        feat2 = seq2[i]
        if feat1 != '-' and feat2 != '-':
            xs = []
            ys = []
            xs.append(ind1[i]) # top left
            ys.append(y1)
            xs.append(ind1[i] + 1) # top right
            ys.append(y1)
            xs.append(ind2[i] + 1) # bottom right
            ys.append(y2)
            xs.append(ind2[i]) #bottom left
            ys.append(y2)
            xs.append(ind1[i]) #top left
            ys.append(y1)
            alpha = 0.5
            if featType in ['CDS', 'gene']:
                try:
                    val = matrix[(feat1, feat2)]
                except:
                    val = matrix[(feat2, feat1)]
                color = cm[val]
                alpha = color[-1]
            elif featType == 'rRNA':
                if feat1 != feat2:
                    alpha=0
            color = colormap[seqname]
            stack1 = np.column_stack([xs, ys])
            myPatches.append(patches.Polygon(stack1, closed=True,
                                             color = color,
                                             alpha = alpha,
                                             lw=0))
    return myPatches