如何在 graphviz/pydot 中实施网格布局？

Question

tl;dr：如何使 graphviz 坚持节点的网格布局？

我正在尝试为时间序列绘制 "full causal graph"。这意味着我有一些图表，其中单位和时间索引在时间方向上重复。

我想用 Graphviz 绘制图形，因为它是程序化的。我不知道单位的数量，也不知道时间步长的数量。随着项目的继续，这将有所不同。我可能还想以编程方式调整颜色、笔划宽度等，作为机器学习模型的可视化。

为了使图表易于阅读，我需要考虑一些布局注意事项：

单位按行排列
列中的时间索引
图中的边周期性地重复（在下图中橙色是垂直的，蓝色是 1 个时间步长，棕色是两个时间步长）

因此，我正在尝试复制此 powerpoint 模型。

为了实现这一点，我从一些'SO post中获得了灵感，并添加了带有 rank=same 的子图以及不可见的边。 post 显示：

从其他 SO posts，我已经能够以我喜欢的方式订购我的节点。当前输出如下。由于我使用的是 pydot，因此 python 代码和点代码非常难看。我会根据要求 link。

如您所见，除了一些怪癖外，一切正常：

1)不可见节点与可见节点不对齐 1) 橙色箭头是弯曲的，因为它们与不可见的箭头相撞

有没有办法让Graphviz优雅地处理这个问题？ 如何强制网格布局，以及如何使橙色箭头笔直？

上图的 Pydot 源代码

import io
import pydot 
import matplotlib.image as img
import matplotlib.pyplot as plt


def render_pydot(g: pydot.Dot, prog):
    # noinspection PyUnresolvedReferences
    png_bytes = g.create(prog=prog, format="png")
    bytes_as_inmemory_file = io.BytesIO(png_bytes)
    img2 = img.imread(bytes_as_inmemory_file)
    plt.figure()
    plt.imshow(img2, aspect='equal')
    plt.axis(False)
    plt.grid(False)
    plt.show()


def create_dot_for_timeseries_with_pydot():
    """Generate a dot object for a static 'full time series'"""
    g = pydot.Dot(rankdir='LR')

    units = ["Alfa", "Beta", "Gamma"]
    time_steps = list(range(0, 5))  # five steps, two invisible
    for t in time_steps:
        sg = pydot.Subgraph(rank="same", rankdir="TB")
        for u, _ in enumerate(units):

            # create nodes
            this_node_name = f"{t}_{u}"
            opts = {'name': this_node_name,
                    'label': this_node_name
                    }
            if t not in time_steps[1:-1]:
                opts['style'] = 'invis'
                opts['color'] = 'gray70'
            n = pydot.Node(**opts)

            # create invisible edges to enforce order vertically and horizontally
            # 
            if u != 0:
                prev = f"{t}_{u - 1}"
                e = pydot.Edge(src=prev, dst=this_node_name,
                               style='invis',
                               color="gray70",
                               weight=1000)
                sg.add_edge(e)

            if t in time_steps[:-1]:
                next = f"{t + 1}_{u}"
                g.add_edge(pydot.Edge(src=this_node_name, dst=next,
                                      style="invis",
                                      color="gray70", weight=1000))

            sg.add_node(n)
        g.add_subgraph(sg)

        # Draw lag 0 effects
        if t in time_steps[1:-1]:
            g.add_edge(pydot.Edge(f"{t}_{0}", f"{t}_{1}", color="orange"))

        # Draw lag 1 effects
        if t in time_steps[:-1]:
            for u, _ in enumerate(units):
                g.add_edge(pydot.Edge(f"{t}_{u}", f"{t + 1}_{u}", color="blue"))
            g.add_edge(pydot.Edge(f"{t}_{0}", f"{t + 1}_{1}", color="blue"))
            g.add_edge(pydot.Edge(f"{t}_{1}", f"{t + 1}_{2}", color="blue"))

        # Draw lag 2 effects
        if t in time_steps[:-2]:
            g.add_edge(pydot.Edge(f"{t}_{0}", f"{t + 2}_{1}", color="brown"))

    return g


g = create_dot_for_timeseries_with_pydot()
print(g) # print the dot document as text for inspection
render_pydot(g, prog='dot') # show the image

从上面 python 文件生成的 DOT 代码

digraph G {
rankdir=LR;
splines=False;
"0_0" -> "1_0"  [color=gray70, style=invis, weight=1000];
"0_1" -> "1_1"  [color=gray70, style=invis, weight=1000];
"0_2" -> "1_2"  [color=gray70, style=invis, weight=1000];
subgraph  {
rank=same;
rankdir=TB;
"0_0" [color=gray70, label="0_0", style=invis];
"0_0" -> "0_1"  [color=gray70, style=invis, weight=1000];
"0_1" [color=gray70, label="0_1", style=invis];
"0_1" -> "0_2"  [color=gray70, style=invis, weight=1000];
"0_2" [color=gray70, label="0_2", style=invis];
}
"0_0" -> "1_0"  [color=blue];
"0_1" -> "1_1"  [color=blue];
"0_2" -> "1_2"  [color=blue];
"0_0" -> "1_1"  [color=blue];
"0_1" -> "1_2"  [color=blue];
"0_0" -> "2_1"  [color=brown];
"1_0" -> "2_0"  [color=gray70, style=invis, weight=1000];
"1_1" -> "2_1"  [color=gray70, style=invis, weight=1000];
"1_2" -> "2_2"  [color=gray70, style=invis, weight=1000];
subgraph  {
rank=same;
rankdir=TB;
"1_0" [label="1_0"];
"1_0" -> "1_1"  [color=gray70, style=invis, weight=1000];
"1_1" [label="1_1"];
"1_1" -> "1_2"  [color=gray70, style=invis, weight=1000];
"1_2" [label="1_2"];
}
"1_0" -> "1_1"  [color=orange];
"1_0" -> "2_0"  [color=blue];
"1_1" -> "2_1"  [color=blue];
"1_2" -> "2_2"  [color=blue];
"1_0" -> "2_1"  [color=blue];
"1_1" -> "2_2"  [color=blue];
"1_0" -> "3_1"  [color=brown];
"2_0" -> "3_0"  [color=gray70, style=invis, weight=1000];
"2_1" -> "3_1"  [color=gray70, style=invis, weight=1000];
"2_2" -> "3_2"  [color=gray70, style=invis, weight=1000];
subgraph  {
rank=same;
rankdir=TB;
"2_0" [label="2_0"];
"2_0" -> "2_1"  [color=gray70, style=invis, weight=1000];
"2_1" [label="2_1"];
"2_1" -> "2_2"  [color=gray70, style=invis, weight=1000];
"2_2" [label="2_2"];
}
"2_0" -> "2_1"  [color=orange];
"2_0" -> "3_0"  [color=blue];
"2_1" -> "3_1"  [color=blue];
"2_2" -> "3_2"  [color=blue];
"2_0" -> "3_1"  [color=blue];
"2_1" -> "3_2"  [color=blue];
"2_0" -> "4_1"  [color=brown];
"3_0" -> "4_0"  [color=gray70, style=invis, weight=1000];
"3_1" -> "4_1"  [color=gray70, style=invis, weight=1000];
"3_2" -> "4_2"  [color=gray70, style=invis, weight=1000];
subgraph  {
rank=same;
rankdir=TB;
"3_0" [label="3_0"];
"3_0" -> "3_1"  [color=gray70, style=invis, weight=1000];
"3_1" [label="3_1"];
"3_1" -> "3_2"  [color=gray70, style=invis, weight=1000];
"3_2" [label="3_2"];
}
"3_0" -> "3_1"  [color=orange];
"3_0" -> "4_0"  [color=blue];
"3_1" -> "4_1"  [color=blue];
"3_2" -> "4_2"  [color=blue];
"3_0" -> "4_1"  [color=blue];
"3_1" -> "4_2"  [color=blue];
subgraph  {
rank=same;
rankdir=TB;
"4_0" [color=gray70, label="4_0", style=invis];
"4_0" -> "4_1"  [color=gray70, style=invis, weight=1000];
"4_1" [color=gray70, label="4_1", style=invis];
"4_1" -> "4_2"  [color=gray70, style=invis, weight=1000];
"4_2" [color=gray70, label="4_2", style=invis];
}
}

Answer 1

我认为这种情况下的诀窍是指定完整的（网格）图，然后使不需要的部分不可见。这是您的案例的一个最小示例。（我刚刚省略了颜色。）

digraph{

# Columns
subgraph {
"0_0" [style=invis]
"0_1" [style=invis]
"0_2" [style=invis]
}

subgraph  {
"1_0"
"1_1"
"1_2"
}

subgraph  {
"2_0"
"2_1"
"2_2"
}

subgraph  {
"3_0"
"3_1"
"3_2"
}

subgraph  {
"4_0" [style=invis]
"4_1" [style=invis]
"4_2" [style=invis]
}

# Rows
subgraph {
rank=same
"0_0"
"1_0"
"2_0"
"3_0"
"4_0"
}

subgraph {
rank=same
"0_1"
"1_1"
"2_1"
"3_1"
"4_1"
}

subgraph {
rank=same
"0_2"
"1_2"
"2_2"
"3_2"
"4_2"
}

# Straight edges
"0_0" -> "1_0"
"0_1" -> "1_1"
"0_2" -> "1_2"

"1_0" -> "2_0"
"1_1" -> "2_1"
"1_2" -> "2_2"

"2_0" -> "3_0"
"2_1" -> "3_1"
"2_2" -> "3_2"

"3_0" -> "4_0"
"3_1" -> "4_1"
"3_2" -> "4_2"

"0_0" -> "0_1" [style=invis]
"1_0" -> "1_1"
"2_0" -> "2_1"
"3_0" -> "3_1"
"4_0" -> "4_1" [style=invis]

"0_1" -> "0_2" [style=invis]
"1_1" -> "1_2" [style=invis]
"2_1" -> "2_2" [style=invis]
"3_1" -> "3_2" [style=invis]
"4_1" -> "4_2" [style=invis]


#  Diagonal edges
"0_0" -> "1_1"
"0_0" -> "2_1"
"1_0" -> "3_1"
"2_0" -> "4_1"
"0_1" -> "1_2"
"1_1" -> "2_2"
"2_1" -> "3_2"
"3_1" -> "4_2"
}

Graphviz output

如何在 graphviz/pydot 中实施网格布局？

How to enforce grid layout in graphviz/pydot?

graphviz

pydot