I have following graph:
digraph G {
rankdir=TB
subgraph cluster_1 {
label = "cluster1"
1; 2; 3; 4; 5; 6; 7; 8; 9; 10;
}
subgraph cluster_2 {
label = "cluster2"
11; 12; 13; 14; 15;
}
subgraph cluster_3 {
label = "cluster3"
16; 17; 18; 19; 20; 21;
}
7 -> {10, 3, 4}
10 -> 9
4 -> {1, 6, 5, 2}
4 -> 13
8 -> {3, 4}
13 -> {11, 12}
11 -> {16, 14, 15}
16 -> {17, 19, 20, 21, 18}
}
The output I see is:
How I can place all clusters strictly vertically?
Unfortunately, there is no single attribute to accomplish what you want. But if you add these 3 lines to your graph:
edge [style=invis]
{6 1} -> 13
{14 15} ->16
You get this:
Related
I have rewitten this as the following,
NN = 2000;
mu = 0;
sigma = 10;
task3a = Table[Random[NormalDistribution[mu,sigma]], {NN}];
ListPlot[task3a, AxesLabel->{" No.obs.", "value of the obs"},
PlotLabel -> " Normal Distribution"];
a= 0.6;
b =-0.45;
task4a = Table [0, {NN}] ;
task4a[[1]] = task3a[[1]];
task4a[[2]] = a*task4a[[1]] +task3a[[2]];
For [i = 3, i <= NN, i++,
task4a[[i]] = a*task4a[[i -1]]
+ b*task4a[[i -2]]
+ task3a[[i]];
]
ListPlot[task4a, AxesLabel -> {"No.obs.", "value of the obs"}, PlotLabel-> "Autoregression process for norm.dist. white noise"];
(**************************************************)
avg = (1/NN) * Sum[task4a[[i]], {1, NN}];
task5a = Table[0, {33}] ;
For [k = 0, k <= 32, k++,
task5a[[k + 1]] = (1/(NN-k)) *
Sum[(task4a[[i]] -avg)*(task4a[[i + k]] - avg), {1, NN-k}] ;
]
ListPlot[task5a, PlotLabel ->"K estimator for AR(2) normal distribution", Joined -> True, PlotRange ->All, AxesLabel -> {"k", "K(k)"}] ;
Error Message
The above code is generating the following error message Sum::itraw,
Looks like, there is some problem with the for loop.
I cannot understand.
As #agentyp mentioned. Problem is sum indexes in two places. After execution of this code program works correctly.
NN = 2000;
mu = 0;
sigma = 10;
task3a = Table[Random[NormalDistribution[mu, sigma]], {NN}];
ListPlot[task3a, AxesLabel -> {" No.obs.", "value of the obs"},
PlotLabel -> " Normal Distribution"];
a = 0.6;
b = -0.45;
task4a = Table[0, {NN}];
task4a[[1]] = task3a[[1]];
task4a[[2]] = a*task4a[[1]] + task3a[[2]];
For[i = 3, i <= NN, i++,
task4a[[i]] = a*task4a[[i - 1]] + b*task4a[[i - 2]] + task3a[[i]];]
ListPlot[task4a, AxesLabel -> {"No.obs.", "value of the obs"},
PlotLabel -> "Autoregression process for norm.dist. white noise"];
(**************************************************)
avg = (1/NN)*
Sum[task4a[[i]], {i, 1, NN}];
task5a = Table[0, {33}];
For[k = 0, k <= 32, k++,
task5a[[k + 1]] = (1/(NN - k))*
Sum[(task4a[[i]] - avg)*(task4a[[i + k]] - avg), {i, 1, NN - k}];]
ListPlot[task5a,
PlotLabel -> "K estimator for AR(2) normal distribution",
Joined -> True, PlotRange -> All, AxesLabel -> {"k", "K(k)"}]
I use the following code to produce a graph using dot in Graphviz. I have manually included the coordinates of nodes, as I require four disjoint subgraphs placed adjacent to one another, as in the picture.
I would love to add labels under each of the subgraphs: $G_0$, $G_1$, etc. Adding label under subgraph creates a box and ignores my coordinates alignment. Is there any other way, like placing arbitrary text at specified coordinates? I use "dot -Teps -Kfdp -n trees -o t.eps" for compilation.
digraph Trees {
node [shape=circle, style="filled", fixedsize=true,width=0.6]; 0; 1;2; 3;4; 5;6; 7; 8;9;10;11;12;13;14;15;
0[pos = "0,1!"]
1[fillcolor=red, pos = "-1,2!"]
2[pos = "1,2!"]
3 [pos = "0,-0.5!"]
5[label=1, fillcolor=red, pos = "2,2!"]
4[label=0, fillcolor=red, pos = "3,1!"]
6[label=2, pos = "4,2!"]
7[label=3, pos = "3, -0.5!"]
9[label=1, fillcolor=red, pos = "5,2!"]
8[label=0, fillcolor=red, pos = "6,1!"]
10[label=2, pos = "7,2!"]
11[label=3, fillcolor=red, pos = "6, -0.5!"]
12[label=1, fillcolor=red, pos = "8,2!"]
13[label=0, fillcolor=green, pos = "9,1!"]
14[label=2, pos = "10, 2!"]
15[label=3, fillcolor=green, pos = "9, -0.5!"]
overlap=false;
fontsize=10;
subgraph 1{
edge [dir=none] 1->0 2->0 3->0;
}
subgraph 2{
edge [color=red] 5->4;
edge[color=black, dir=none] 6->4 7->4;
}
subgraph 3{
edge [color=red] 9->8 8->11;
edge [color=black, dir=none] 8->10;
}
subgraph 4{
edge [color=green] 12->13; 13->15;
edge [color=black, dir=none] 13->14;
}
}
The sub-graphs can be made disjoint using clusters and the dot layout engine. The same approach will also permit the introduction of cluster labels. They can be placed at the bottom of the cluster as required without creating dummy nodes.
This way, no absolute positions are required, and, the layout is automatically generated even if other nodes are added. The exact position of the nodes change, but the graphs remain topologically unchanged.
digraph Trees { node [shape = circle, style = "filled", fixedsize = true, width=0.4];
edge [dir = none];
layout = dot; overlap = false; fontsize = 10;
graph [labelloc = "b", penwidth = 0];
{ node [fillcolor = "red"];
1; 5 [label = 1]; 4 [label = 0]; 9 [label = 1];
8 [label = 0]; 11 [label = 3]; 12 [label = 1];
}
2; 0; 3; 6 [label = 2]; 7 [label = 3];
10 [label = 2]; 14 [label = 2];
{ node [fillcolor = "green"];
13 [label = 0]; 15 [label = 3];
}
subgraph cluster1{
label = "Subgraph 1";
{ 1; 2; } -> 0 -> 3;
}
subgraph cluster2{
label = "Subgraph 2";
5 -> 4 [color = red, dir = fwd];
6 -> 4 -> 7;
}
subgraph cluster3{
label = "Subgraph 3";
9 -> 8-> 11 [color=red, dir = fwd];
10 -> 8 [color=black];
}
subgraph cluster4{
label = "Subgraph 4";
12 -> 13 -> 15 [color=green, dir = fwd];
14-> 13;
}
}
Instead of using explicit node positions, you may use a simple directed graph combined with some rank constraints, invisible edges and text nodes instead of subgraph labels:
digraph Trees {
fontsize=10;
node [shape=circle, style="filled", fixedsize=true,width=0.6];
{rank=same;
a1[label=1, fillcolor=red];
a2[label=2];
a3[label=1, fillcolor=red];
a4[label=2];
a5[label=1, fillcolor=red];
a6[label=2];
a7[label=1, fillcolor=red];
a8[label=2];
}
node[label=0];
b1;
b2[fillcolor=red];
b3[fillcolor=red];
b4[fillcolor=green];
node[label=3];
c1;
c2;
c3[fillcolor=red];
c4[fillcolor=green];
node[shape=none, fillcolor=transparent];
d1[label="Label 1"];
d2[label="Label 2"];
d3[label="Label 3"];
d4[label="Label 4"];
edge[dir=none];
a1->b1;
a2->b1;
b1->c1;
c1->d1[style=invis];
a3->b2[dir=forward, fillcolor=red, color=red];
a4->b2;
b2->c2;
c2->d2[style=invis];
a5->b3[dir=forward, fillcolor=red, color=red];
a6->b3[dir=forward, fillcolor=red, color=red];
b3->c3;
c3->d3[style=invis];
a7->b4[dir=forward, fillcolor=green, color=green];
a8->b4[dir=forward, fillcolor=green, color=green];
b4->c4;
c4->d4[style=invis];
edge[style=invis];
a2 -> a3;
a4 -> a5;
a6 -> a7;
}
I can't get GraphViz to respect some node positions, even though they have pos attributes with !. E.g.:
digraph Versions {
ranksep=0.05;
node [style=filled, shape=point, fillcolor=black, fixedsize=true, width=0.3, height=0.1, fontname="Helvetica", fontsize=8, fontcolor=white];
edge [arrowhead=none, len=0.1];
2 [pos="0,0!", fillcolor=red];
3 [pos="20,0!", fillcolor=red];
4 [pos="40,0!", fillcolor=red];
5 [pos="60,0!", fillcolor=red];
6 [pos="80,0!", fillcolor=red];
7 [pos="100,0!", fillcolor=red];
8 [pos="120,0!", fillcolor=red];
9 [pos="140,0!", fillcolor=red];
10 [pos="160,0!", fillcolor=red];
11 [pos="180,0!", fillcolor=red];
12 [pos="200,0!", fillcolor=red];
13 [pos="220,0!", fillcolor=red];
2 -> 14;
14 -> 15;
3 -> 16;
16 -> 17;
11 -> 18;
18 -> 19;
6 -> 20;
20 -> 21;
10 -> 22;
22 -> 23;
13 -> 24;
24 -> 25;
9 -> 26;
26 -> 27;
4 -> 28;
28 -> 29;
7 -> 30;
30 -> 31;
5 -> 32;
32 -> 33;
8 -> 34;
34 -> 35;
12 -> 36;
36 -> 37;
15 -> 38;
38 -> 39;
17 -> 40;
40 -> 41;
19 -> 42;
42 -> 43;
// etc.
}
The top most rank should be evenly distributed, but is not. The horizontal spacing between the top most nodes is not the same:
From the documentation of the pos attribute:
In neato and fdp, pos can be used to set the initial position of a node.
Are you using neato or fdp? Because dot does not respect this attribute.
Assuming you're using neato, here's an excerpt from the manual:
-n[1|2] (no-op) If set, neato assumes nodes have already been positioned and all nodes have a pos attribute giving the positions
This means you can render a graph with
neato -n2 -Tpng mygraph.gv -o mygraph.png
and have neato respect the pos attributes (in points) of the nodes.
This also states that all nodes must have a pos attribute.
Since some nodes of your graph do not have a pos attribute, this will lead to an error.
I have read this link --> Forcing "main line" nodes into a straight line in Graphviz (or alternatives)
Despite using this - I can not get this right. What do I do wrong?
Why is not the node number 3 at the same level=height when I have put the weight at the same as no 2? Why is node 5 not at the same level=height as no 4 dispite using the same weight?
Is there any why to have the same left margin with the boxes 1 and 4
Thanks!
F
<graphviz>
digraph MMM8
{
rankdir=LR
node [shape=box, width="0.8", height="0.5", fontsize="10"];
edge [weight=2]
1, 2, 3, 6, 7;
edge [weight=1]
4, 5, Nod1, 8;
node [shape = box];
1 [label = "111111111111"];
2 [label = "2"];
3 [label = "3"];
4 [label = "4"];
5 [label = "5"];
6 [label = "6"];
7 [label = "7"];
8 [label = "7"];
9 [label = "9"];
Nod1 [label="N1", shape=diamond,style=filled,label="",height=.1,width=.1] ;
{
1-> 2[label="C1"]
2-> 3
3 -> Nod1
4->Nod1
Nod1->5
5->6
6-> 7
5->8
8-> 9
9-> 7
{
rank = same;
1, 4
}
{
rank = same;
6,8
}
}
</graphviz>
You've got to create a subgroup with rank=same and include each node you want inline in the subgroup.
digraph MMM8
{
rankdir=LR
node [shape=box, width="0.8", height="0.5", fontsize="10"];
node [shape = box];
{
rank=same;
1 [label = "111111111111"];
2 [label = "2"];
3 [label = "3"];
6 [label = "6"];
7 [label = "7"];
}
{
rank=same;
4 [label = "4"];
5 [label = "5"];
8 [label = "8"];
Nod1 [label="N1", shape=diamond,style=filled,label="",height=.1,width=.1] ;
}
9 [label = "9"];
1-> 2[label="C1"];
2-> 3;
3 -> Nod1;
4->Nod1;
Nod1->5;
5->6 ;
6-> 7;
5->8;
8-> 9;
9-> 7;
}
If you want to get all those nodes in line, then you'll have to combine the two subgroups into one and move node 9 into it.
I have a test graph here that I would like to tweak to make it look nicer.
Here is the graphviz (dot) source, test6.dot:
digraph G {
ranksep=0.3; size="6.0,6.0";
node [fontsize=11];
subgraph clusterA {
X2 [shape=box];
node [style=filled];
1 -> 2 -> 3 -> X2 -> 5;
6;
7;
label = "A";
color=blue
}
X1 [shape=box];
subgraph clusterB {
node [style=filled];
8;
9;
10 -> 11 -> 12;
12 -> 9;
12 -> 8 -> 13;
13 -> 14;
label = "B";
color=blue
}
subgraph clusterC {
label = "C";
{
node [style="invis"];
gap;
}
node [shape=box];
edge [style="invis"];
X3 -> gap -> X4;
}
14 -> X4 -> 3;
6 -> X1 -> 10;
{ edge [dir="both"];
8 -> X3 -> 7;
}
9 -> X3
}
Questions / changes I would like to make:
I want the flow of nodes 10 -> 11 -> 12 -> 8 -> 13 -> 14 to be in a vertical line (swap 8 and 9 horizontally). How can I do this? (same with 1 -> 2 -> 3 -> X2 -> 5; swap 6 and 1)
I want X1 to be at the same vertical position as 10, and the same horizontal position as 6. How can I do this?
I want 8 and X3 and 7 to be at the same vertical position, also with 14 and X4 and 3. How can I do this?
The ranksep=0.3; statement works great except note that 8 -> 13 -> 14 has a larger gap, as does X3 -> gap -> X4. Why doesn't it obey the ranksep=0.3 rule, and how do I fix this?
Below is the best I can do: phantom nodes and edges help. But I can't seem to encourage a particular ordering in the transverse direction (the other direction from rankdir).
digraph G {
ranksep=0.3; size="6.0,6.0";
rankdir=TB;
node [fontsize=11];
subgraph clusterA {
X2 [shape=box];
label = "A";
color=blue;
node [style=filled];
/* force 1, 6, and 7 to be at the top together,
add enough phantoms to keep things in nice columns */
{
node [style="invis", label=""];
phantom3;
phantom4;
phantom5;
phantom6;
}
rank = same;
1 -> 2 -> 3 -> X2 -> 5;
edge [style="invis"];
6 -> phantom3 -> phantom5;
7 -> phantom4 -> phantom6;
}
subgraph clusterB {
node [style=filled];
label = "B";
color=blue;
/* create an invisible phantom node
to take up space */
{
node [style="invis",label=""];
phantom1;
phantom1b;
}
{ rank=same; 11;
phantom1;
}
10 -> 11 -> 12 -> 8 -> 13 -> 14;
12 -> 9;
phantom1 -> 9 -> phantom1b [style="invis"];
}
/* force X1 to be at the same vertical pos as 10
(this yields a warning though) */
{ rank = same;
X1 [shape=box];
10;
}
6 -> X1;
X1 -> 10 [weight=0.5];
subgraph clusterC {
label = "C";
phantom2 [style="invis", label=""];
node [shape=box];
edge [style="invis"];
X3 -> phantom2 -> X4;
}
9 -> X3 [weight=0.5];
{
edge [weight=20];
14 -> X4 -> 3;
3 -> X4 -> 14 [style="invis"];
/* add a reverse path so graphviz doesn't force 14 above X4 above 3 */
}
{
edge [dir="both", weight=20];
8 -> X3 -> 7;
7 -> X3 -> 8 [style="invis"];
edge [style="invis"];
X4 -> phantom6;
1 -> phantom2;
8 -> phantom2;
}
}