How can i place the following diagram with subgraphs layout horizontally, not vertically?
Up until now I had the understanding that rankdir parameter is responsible for that - and that's why I've set it to LR. However this does not work.
I've been trying to fiddle around with ratio options, but none of those tried gave anything useful.
digraph {
rankdir=LR
ratio="expand"
subgraph cluster_3 {
label=C
style=filled
color=lightgrey
"39649811_plecak-nike-szkolny-sportowy-ba5405-010-b-r_after_time_decay"
"10023965_wojna-swiatow-wells-vesper-twarda-oprawa_after_time_decay"
"11097750_aldous-huxley-nowy-wspanialy-swiat-________after_time_decay"
"11097750_stanislaw-lem-pamietnik-znaleziony-w-wannie-______after_time_decay"
"6740469_pozdrawiam-moje-miasto-jozef-ratajczak-1968_after_time_decay"
"6740469_nowy-korbut-bibliografia-literatury-polskiej-14-t_after_time_decay"
"6740469_superkomputery-bez-tajemnic-david-loshin-1997_after_time_decay"
"21424429_wojny-w-cyberprzestrzeni-guisnel-jean-znak_after_time_decay"
"38901148_koniec-swieta-eisuke-nakazono_after_time_decay"
"17346660_podstawy-informatyki-kolodziejczak-zielinski_after_time_decay"
"6740469_urzadzenie-wewnetrzne-miast-wolnych-sejm-wielki_after_time_decay"
"15528768_ddd-kompendium-wiedzy-vaughn-vernon_after_time_decay"
"138008_matematyka-dyskretna-dla-informatykow_after_time_decay"
"45702657_polski-fiat-125pfso-125p_after_time_decay"
"43306282_unity-w-akcji-joe-hocking_after_time_decay"
"46889202_eng-victor-eijkhout-tex-by-topic_after_time_decay"
"4276139_wallace-wang-internet-hakerzy-wirusy-ladnyegz_after_time_decay"
"38901148_micro-prolog-keith-l-clark_after_time_decay"
"46889202_eng-victor-eijkhout-tex-by-topic_after_time_decay"
}
subgraph cluster_2 {
label=B
style=filled
color=lightgrey
"39649811_plecak-nike-szkolny-sportowy-ba5405-010-b-r"
"10023965_wojna-swiatow-wells-vesper-twarda-oprawa"
"11097750_aldous-huxley-nowy-wspanialy-swiat-_______"
"11097750_stanislaw-lem-pamietnik-znaleziony-w-wannie-_____"
"6740469_pozdrawiam-moje-miasto-jozef-ratajczak-1968"
"6740469_nowy-korbut-bibliografia-literatury-polskiej-14-t"
"6740469_superkomputery-bez-tajemnic-david-loshin-1997"
"21424429_wojny-w-cyberprzestrzeni-guisnel-jean-znak"
"38901148_koniec-swieta-eisuke-nakazono"
"17346660_podstawy-informatyki-kolodziejczak-zielinski"
"6740469_urzadzenie-wewnetrzne-miast-wolnych-sejm-wielki"
"6740469_superkomputery-bez-tajemnic-david-loshin-1997"
"15528768_ddd-kompendium-wiedzy-vaughn-vernon"
"138008_matematyka-dyskretna-dla-informatykow"
"45702657_polski-fiat-125pfso-125p"
"43306282_unity-w-akcji-joe-hocking"
"46889202_eng-victor-eijkhout-tex-by-topic"
"4276139_wallace-wang-internet-hakerzy-wirusy-ladnyegz"
"38901148_micro-prolog-keith-l-clark"
"46889202_eng-victor-eijkhout-tex-by-topic"
}
subgraph cluster_1 {
label=A
style=filled
color=lightgrey
7440293919
7316212119
7459478910
7496246732
7220215448
7030101965
7307790911
7498596862
7465256747
7477936369
6957447807
7307790911
7426854990
7476186414
7152887795
7318012429
7195398720
7474847554
6968472561
7195397122
}
7440293919 -> "39649811_plecak-nike-szkolny-sportowy-ba5405-010-b-r" [label="2018-08-13T15:43:02.127" constraint=false]
7316212119 -> "10023965_wojna-swiatow-wells-vesper-twarda-oprawa" [label="2018-08-11T23:54:52.740" constraint=false]
7459478910 -> "11097750_aldous-huxley-nowy-wspanialy-swiat-_______" [label="2018-08-11T23:53:55.626" constraint=false]
7496246732 -> "11097750_stanislaw-lem-pamietnik-znaleziony-w-wannie-_____" [label="2018-08-11T23:53:21.720" constraint=false]
7220215448 -> "6740469_pozdrawiam-moje-miasto-jozef-ratajczak-1968" [label="2018-08-11T23:52:12.432" constraint=false]
7030101965 -> "6740469_nowy-korbut-bibliografia-literatury-polskiej-14-t" [label="2018-08-11T23:52:08.754" constraint=false]
7307790911 -> "6740469_superkomputery-bez-tajemnic-david-loshin-1997" [label="2018-08-11T23:52:03.990" constraint=false]
7498596862 -> "21424429_wojny-w-cyberprzestrzeni-guisnel-jean-znak" [label="2018-08-11T23:05:59.337" constraint=false]
7465256747 -> "38901148_koniec-swieta-eisuke-nakazono" [label="2018-08-11T23:04:31.077" constraint=false]
7477936369 -> "17346660_podstawy-informatyki-kolodziejczak-zielinski" [label="2018-08-11T23:02:58.123" constraint=false]
6957447807 -> "6740469_urzadzenie-wewnetrzne-miast-wolnych-sejm-wielki" [label="2018-08-11T23:01:58.357" constraint=false]
7307790911 -> "6740469_superkomputery-bez-tajemnic-david-loshin-1997" [label="2018-08-11T23:01:42.263" constraint=false]
7426854990 -> "15528768_ddd-kompendium-wiedzy-vaughn-vernon" [label="2018-08-11T22:55:01.702" constraint=false]
7476186414 -> "138008_matematyka-dyskretna-dla-informatykow" [label="2018-08-11T22:54:26.675" constraint=false]
7152887795 -> "45702657_polski-fiat-125pfso-125p" [label="2018-08-11T22:47:26.011" constraint=false]
7318012429 -> "43306282_unity-w-akcji-joe-hocking" [label="2018-08-11T22:45:34.938" constraint=false]
7195398720 -> "46889202_eng-victor-eijkhout-tex-by-topic" [label="2018-08-11T22:44:44.794" constraint=false]
7474847554 -> "4276139_wallace-wang-internet-hakerzy-wirusy-ladnyegz" [label="2018-08-11T22:42:30.278" constraint=false]
6968472561 -> "38901148_micro-prolog-keith-l-clark" [label="2018-08-11T22:41:27.522" constraint=false]
7195397122 -> "46889202_eng-victor-eijkhout-tex-by-topic" [label="2018-08-11T22:39:47.893" constraint=false]
"39649811_plecak-nike-szkolny-sportowy-ba5405-010-b-r" -> "39649811_plecak-nike-szkolny-sportowy-ba5405-010-b-r_after_time_decay" [label=0.8711024820449741 constraint=false]
"10023965_wojna-swiatow-wells-vesper-twarda-oprawa" -> "10023965_wojna-swiatow-wells-vesper-twarda-oprawa_after_time_decay" [label=0.7220784976320539 constraint=false]
"11097750_aldous-huxley-nowy-wspanialy-swiat-_______" -> "11097750_aldous-huxley-nowy-wspanialy-swiat-________after_time_decay" [label=0.7220292630457892 constraint=false]
"11097750_stanislaw-lem-pamietnik-znaleziony-w-wannie-_____" -> "11097750_stanislaw-lem-pamietnik-znaleziony-w-wannie-______after_time_decay" [label=0.7220000378705059 constraint=false]
"6740469_pozdrawiam-moje-miasto-jozef-ratajczak-1968" -> "6740469_pozdrawiam-moje-miasto-jozef-ratajczak-1968_after_time_decay" [label=0.7219403226503834 constraint=false]
"6740469_nowy-korbut-bibliografia-literatury-polskiej-14-t" -> "6740469_nowy-korbut-bibliografia-literatury-polskiej-14-t_after_time_decay" [label=0.72193715306945 constraint=false]
"6740469_superkomputery-bez-tajemnic-david-loshin-1997" -> "6740469_superkomputery-bez-tajemnic-david-loshin-1997_after_time_decay" [label=0.7219330476524938 constraint=false]
"21424429_wojny-w-cyberprzestrzeni-guisnel-jean-znak" -> "21424429_wojny-w-cyberprzestrzeni-guisnel-jean-znak_after_time_decay" [label=0.7195584388992393 constraint=false]
"38901148_koniec-swieta-eisuke-nakazono" -> "38901148_koniec-swieta-eisuke-nakazono_after_time_decay" [label=0.7194828881206028 constraint=false]
"17346660_podstawy-informatyki-kolodziejczak-zielinski" -> "17346660_podstawy-informatyki-kolodziejczak-zielinski_after_time_decay" [label=0.7194033364179696 constraint=false]
"6740469_urzadzenie-wewnetrzne-miast-wolnych-sejm-wielki" -> "6740469_urzadzenie-wewnetrzne-miast-wolnych-sejm-wielki_after_time_decay" [label=0.7193521968901969 constraint=false]
"15528768_ddd-kompendium-wiedzy-vaughn-vernon" -> "15528768_ddd-kompendium-wiedzy-vaughn-vernon_after_time_decay" [label=0.7189958827772579 constraint=false]
"138008_matematyka-dyskretna-dla-informatykow" -> "138008_matematyka-dyskretna-dla-informatykow_after_time_decay" [label=0.7189659445411196 constraint=false]
"45702657_polski-fiat-125pfso-125p" -> "45702657_polski-fiat-125pfso-125p_after_time_decay" [label=0.7186065898565137 constraint=false]
"43306282_unity-w-akcji-joe-hocking" -> "43306282_unity-w-akcji-joe-hocking_after_time_decay" [label=0.7185117650305968 constraint=false]
"46889202_eng-victor-eijkhout-tex-by-topic" -> "46889202_eng-victor-eijkhout-tex-by-topic_after_time_decay" [label=0.7184689644772201 constraint=false]
"4276139_wallace-wang-internet-hakerzy-wirusy-ladnyegz" -> "4276139_wallace-wang-internet-hakerzy-wirusy-ladnyegz_after_time_decay" [label=0.7183541723056891 constraint=false]
"38901148_micro-prolog-keith-l-clark" -> "38901148_micro-prolog-keith-l-clark_after_time_decay" [label=0.7183006310417779 constraint=false]
"46889202_eng-victor-eijkhout-tex-by-topic" -> "46889202_eng-victor-eijkhout-tex-by-topic_after_time_decay" [label=0.7182156473959604 constraint=false]
}
Related
I try to represent a graph called "dynamic Bayesian network". This graph is composed of a sequence of cluster representing different timeslices (from 0 to N). In each timeslice, I would have the same node, in the same order. Edges only are between nodes in the same timeslice or from a timeslice to the next one.
For instance :
However, from time to time, the ordering of the clusters is not correct. Here timeslice 2 is before timeslice 1 ...
Here is the dot file I have for the second one :
digraph G {
rankdir=TD;
splines=ortho;
node [color="#000000", fillcolor=white, style=filled];
subgraph cluster_0 {
bgcolor="#DDDDDD";
label="Time slice 0";
rankdir=TD;
"P0" [label="P"];
"R0" [label="R"];
"dP0" [label="dP"];
"dR0" [label="dR"];
}
subgraph cluster_1 {
bgcolor="#DDDDDD";
label="Time slice 1";
rankdir=TD;
"P1" [label="P"];
"R1" [label="R"];
"dP1" [label="dP"];
"dR1" [label="dR"];
}
subgraph cluster_2 {
bgcolor="#DDDDDD";
label="Time slice 2";
rankdir=TD;
"P2" [label="P"];
"R2" [label="R"];
"dP2" [label="dP"];
"dR2" [label="dR"];
}
edge [color=blue, constraint=False];
"P0" -> "P1";
"P1" -> "dP1";
"P2" -> "dP2";
"R1" -> "R2";
"R1" -> "dP1";
"R0" -> "dP0";
"dR1" -> "R2";
"R2" -> "dR2";
"dR0" -> "R1";
"dP1" -> "P2";
"P0" -> "dP0";
"P1" -> "P2";
"R2" -> "dP2";
"R0" -> "dR0";
"dP0" -> "P1";
"R0" -> "R1";
"P0" -> "dR0";
"P1" -> "dR1";
"P2" -> "dR2";
"R1" -> "dR1";
edge [constraint=True, style=invis];
"P0" -> "R0";
"R0" -> "dP0";
"dP0" -> "dR0";
"P1" -> "R1";
"R1" -> "dP1";
"dP1" -> "dR1";
"P2" -> "R2";
"R2" -> "dP2";
"dP2" -> "dR2";
}
If I try just to add constraints such as "P0->P1;P1->P2", the order is correct but the clusters are not aligned any more ...
Does someone know how to fix the ordering between the clusters in this graph ?
Changed rankdir direction to guarantee correct sequence of clusters. That in-turn forced rank=same within each cluster, plus a few other tweaks.
digraph G {
rankdir=LR // was rankdir=TD;
splines=ortho;
node [color="#000000", fillcolor=white, style=filled];
subgraph cluster_0 {
bgcolor="#DDDDDD";
label="Time slice 0";
// only applies to Root graph: rankdir=TD;
{rank=same // because we changed rankdir
"P0" [label="P"];
"R0" [label="R"];
"dP0" [label="dP"];
"dR0" [label="dR"];
}
}
subgraph cluster_1 {
bgcolor="#DDDDDD";
label="Time slice 1";
{rank=same
"P1" [label="P"];
"R1" [label="R"];
"dP1" [label="dP"];
"dR1" [label="dR"];
}
}
subgraph cluster_2 {
bgcolor="#DDDDDD";
label="Time slice 2";
{rank=same
"P2" [label="P"];
"R2" [label="R"];
"dP2" [label="dP"];
"dR2" [label="dR"];
}
}
edge [color=blue, constraint=False];
"P0" -> "P1";
"P1" -> "dP1";
"P2" -> "dP2";
"R1" -> "R2";
"R1" -> "dP1";
"R0" -> "dP0";
"dR1" -> "R2";
"R2" -> "dR2";
"dR0" -> "R1";
"dP1" -> "P2";
"P0" -> "dP0";
"P1" -> "P2";
"R2" -> "dP2";
"R0" -> "dR0";
"dP0" -> "P1";
"R0" -> "R1";
"P0" -> "dR0";
"P1" -> "dR1";
"P2" -> "dR2";
"R1" -> "dR1";
// establish positions
edge [style=invis constraint=true]
P0 -> P1 -> P2
R0 -> R1 -> R2
dP0 -> dP1 -> dP2
dR0 -> dR1 -> dR2
}
Giving:
I am trying to inverse the position of two nodes (producción & funciones) that are inside a cluster (cluster_fp). Instead of producción on top and funciones at bottom, I need funciones on top and producción at bottom. How can I achieve that? They are in a cluster just because I thought it is the right approach, but probably it isn't. Because my reputation, I can't post images directly, so I leave the links to i.stack.imgur.com.
Code:
digraph tríada {
rankdir=LR;
edge [arrowhead=none];
label="* socialmente reconocido";
labeljust=left;
subgraph cluster_sinonimia_oa {
style=dashed;
label="sinonimia obra-texto";
subgraph cluster_texto {
style=striped;
label=texto;
selección [shape=rect];
}
obra [shape=rect, style=striped];
supuesto [label="supuesto\nexistencial", shape=plain];
}
subgraph cluster_autor {
style=striped;
label="autor*";
máquinas [shape=hexagon];
subgraph cluster_fp {
label="";
style=invis;
funciones [label="atribución o\napropiación", shape=plain];
producción [shape=plain];
}
subgraph cluster_sinonimia_nepa {
style=dashed;
label="sinonimia nombre-entidad-persona-autor";
personas [shape=hexagon];
entidad [shape=rect];
real [shape=diamond];
ficticia [shape=diamond];
nula [shape=diamond];
denotación [shape=plain];
nombre [shape=rect];
}
}
{personas máquinas} -> real [arrowhead=normal];
{real ficticia nula} -> entidad [arrowhead=normal];
nombre -> funciones -> obra -> supuesto -> selección -> producción -> entidad -> denotación -> nombre;
}
Live on dreampuf.github.io
Thanks!
Based on lots of experiments, the problem seems to be that dot's algorithm "weights" a multi-node edge more than a two-node edge.
Here is a much-edited input file that produces your desired output:
digraph tríada {
rankdir=LR;
edge [arrowhead=none];
label="* socialmente reconocido";
labeljust=left;
subgraph cluster_autor {
style=striped;
label="autor*";
subgraph cluster_sinonimia_nepa {
style=dashed;
label="sinonimia nombre-entidad-persona-autor";
personas [shape=hexagon];
entidad [shape=rect];
real [shape=diamond];
ficticia [shape=diamond];
nula [shape=diamond];
denotación [shape=plain];
nombre [shape=rect];
node [label="" shape=point width=.01]
// bogus1 & bogus2 are needed to flip/swap/invert the funciones & producción nodes
bogus1 bogus2
}
subgraph cluster_fp {
label="";
style=invis;
funciones [label="atribución o\napropiación", shape=plain];
producción [shape=plain];
}
máquinas [shape=hexagon];
{personas máquinas} -> real [arrowhead=normal];
{real ficticia nula} -> entidad [arrowhead=normal];
entidad -> denotación -> nombre
}
subgraph cluster_sinonimia_oa {
style=dashed;
label="sinonimia obra-texto";
subgraph cluster_texto {
style=striped;
label=texto;
selección [shape=rect];
}
obra [shape=rect, style=striped];
supuesto [label="supuesto\nexistencial", shape=plain];
}
nombre -> funciones -> obra -> supuesto -> selección
producción -> selección
entidad -> bogus1 [headclip=false ]
bogus1 -> bogus2 [tailclip=false, headclip=false]
bogus2 -> producción [tailclip=false]
}
(Yes, most of the edits were unnecessary)
On my graph, any two edges between the same two nodes are drawn over each other without any gap between them whatsoever. Basically, they completely overlap and appear as a single edge.
.
What appears to be a single bidirectional edge between "leutkeni" and "mazatlanensis" are in fact two unidirectional arrows that have been rendered on top of each other.
Here's the code (I use the circo engine):
digraph {
splines=true;
esep=0.3
mindist=1.4
edge [len=2,fontsize=16,fontcolor=blue]
node [fontsize=20,shape=circle,width=1.5]
canaliferus -> nebulifer
mazatlanensis -> canaliferus
valliceps -> mazatlanensis
houstonensis -> woodhousii
nebulifer -> arenarum
mazatlanensis -> nebulifer
woodhousii -> houstonensis
houstonensis -> americanus
boreas -> canorus
marmoreus -> mazatlanensis
garmani -> regularis
boreas -> alvarius
hemiophrys -> boreas
hemiophrys -> mazatlanensis
houstonensis -> terrestris
punctatus -> marmoreus
mazatlanensis -> marmoreus
nebulifer -> peltacephalus
woodhousii -> luetkeni
paracnemis -> arenarum
mazatlanensis -> valliceps
boreas -> marmoreus
brauni -> garmani
americanus -> bocourti
boreas -> mazatlanensis
nebulifer -> luetkeni
luetkeni -> cognatus
woodhousii -> ictericus
boreas -> alvarius
arenarum -> nebulifer
hemiophrys -> calamita
terrestris -> viridis
woodhousii -> punctatus
nebulifer -> granulosus
luetkeni -> mazatlanensis
woodhousii -> calamita
garmani -> brauni
coccifer -> punctatus
mazatlanensis -> luetkeni
cognatus -> calamita
speciosus -> canorus
punctatus -> speciosus
woodhousii -> coccifer
americanus -> marmoreus
nebulifer -> cognatus
arenarum -> spinulosus
regularis-> garmani
woodhousii -> arenarum
nebulifer -> canaliferus
luetkeni -> nebulifer
terrestris -> quercicus
woodhousii -> viridis
terrestris -> mazatlanensis
coccifer -> nebulifer
speciosus -> arenarum
speciosus -> ibarrai
terrestris -> woodhousii
marmoreus -> beebei
regularis -> speciosus
hemiophrys -> americanus
marinus -> paracnemis
boreas -> viridis
hemiophrys -> bufo
canaliferus -> valliceps
boreas -> ibarrai
poeppigi -> marinus
canorus -> marmoreus
terrestris -> calamita
coccifer -> luetkeni
melanostictus -> coniferus
guttaralis -> regularis
cognatus -> bocourti
regularis -> speciosus
nebulifer -> bocourti
canorus -> stomaticus
arunco -> valliceps
canaliferus -> coccifer
luetkeni -> microscaphus
nebulifer -> ibarrai
boreas -> bocourti
hemiophrys -> cognatus
boreas -> nebulifer
woodhousii -> bocourti
coccifer -> marmoreus
regularis -> canaliferus
regularis -> arenarum
arenarum -> paracnemis
}
I have tried and can tell that the issue resolves itself when I set "splines=false" (there immediately appears some space between edges connecting the same nodes), but I need splines set at true because I need curved edges.
It is fixable with splines set at true?
What version are you using? this problem is not on http://viz-js.com/
The trig I usual apply is to use a compass port on one of the edges e.g.
leutkeni:w->mazatlanensis
I have the following .dot file.
digraph
{
node [color=Limegreen,fontcolor=Limegreen,shape=oval]
ilocus [label="iLocus"]
gilocus [label="giLocus"]
pilocus [label="piLocus"]
nilocus [label="niLocus"]
silocus [label="siLocus"]
cilocus [label="ciLocus"]
filocus [label="fiLocus"]
iilocus [label="iiLocus"]
node [color=Blue,fontcolor=Blue,shape=diamond]
containgene [label="Contains gene(s)?"]
proteincoding [label="Protein coding?"]
multiplegenes [label="Multiple genes?"]
geneflank [label="Flanked by genes\non both sides?"]
ilocus -> containgene
containgene:e -> geneflank [xlabel="No"]
geneflank:e -> filocus [xlabel="No"]
geneflank:w -> iilocus [xlabel="Yes"]
containgene:w -> gilocus [xlabel="Yes"]
gilocus -> proteincoding
proteincoding:e -> nilocus [xlabel="No"]
proteincoding:w -> pilocus [xlabel="Yes"]
pilocus -> multiplegenes
multiplegenes:e -> silocus [xlabel="No"]
multiplegenes:w -> cilocus [xlabel="Yes"]
}
Rendering with graphviz I get the following.
Is there any way I can force the edges to have square corners rather than rounded corners? The splines=ortho attribute from the documentation seems to be designed for this in principle, but in practice I just get straight lines when I add graph [splines=ortho] to my digraph.
Any way I can get square corners on the edges with graphviz? Something like the following:
------ Multiple genes? -----
| |
| N Y |
| |
v V
siLocus ciLocus
Maybe you can start out by using splines=line
digraph
{
splines=line
...
which will give you this graph:
From there you might need to manually position the nodes, or insert hidden nodes and edges like
digraph
{
splines=line
node [color=Limegreen,fontcolor=Limegreen,shape=oval]
ilocus [label="iLocus"]
gilocus [label="giLocus"]
pilocus [label="piLocus"]
nilocus [label="niLocus"]
silocus [label="siLocus"]
cilocus [label="ciLocus"]
filocus [label="fiLocus"]
iilocus [label="iiLocus"]
node [color=Blue,fontcolor=Blue,shape=diamond]
containgene [label="Contains gene(s)?"]
proteincoding [label="Protein coding?"]
multiplegenes [label="Multiple genes?"]
geneflank [label="Flanked by genes\non both sides?"]
spacer1 [label="xxxx",style=invis]
{rank=same gilocus spacer1 geneflank}
gilocus -> spacer1 -> geneflank [style=invis]
ilocus -> containgene
containgene:e -> geneflank [xlabel="No"]
geneflank:e -> filocus [xlabel="No"]
geneflank:w -> iilocus [xlabel="Yes"]
containgene:w -> gilocus [xlabel="Yes"]
gilocus -> proteincoding
proteincoding:e -> nilocus [xlabel="No"]
proteincoding:w -> pilocus [xlabel="Yes"]
pilocus -> multiplegenes
multiplegenes:e -> silocus [xlabel="No"]
multiplegenes:w -> cilocus [xlabel="Yes"]
}
which produces
Alternatively, you can insert spaces in the top labels to make lower nodes line up better:
digraph
{
splines=line
node [color=Limegreen,fontcolor=Limegreen,shape=oval]
ilocus [label="iLocus"]
gilocus [label="giLocus"]
pilocus [label="piLocus"]
nilocus [label="niLocus"]
silocus [label="siLocus"]
cilocus [label="ciLocus"]
filocus [label="fiLocus"]
iilocus [label="iiLocus"]
node [color=Blue,fontcolor=Blue,shape=diamond]
containgene [label=" Contains gene(s)? "]
proteincoding [label="Protein coding?"]
multiplegenes [label="Multiple genes?"]
geneflank [label="Flanked by genes\non both sides?"]
ilocus -> containgene
containgene:e -> geneflank [xlabel="No"]
geneflank:e -> filocus [xlabel="No"]
geneflank:w -> iilocus [xlabel="Yes"]
containgene:w -> gilocus [xlabel="Yes"]
gilocus -> proteincoding
proteincoding:e -> nilocus [xlabel="No"]
proteincoding:w -> pilocus [xlabel="Yes"]
pilocus -> multiplegenes
multiplegenes:e -> silocus [xlabel="No"]
multiplegenes:w -> cilocus [xlabel="Yes"]
}
which produces
You may simply use splines=false (link to GraphvizFiddle).
I'm trying to get multiple clusters of nodes to space evenly in Graphviz.
I think the image best explains what I'm trying to do:
As you can see from the image, there is extra spacing between layers 2 and 3. The space between 2 and 3 should be the same as the space between 1 and 2.
The spacing also needs to scale with more than 3 layers. When I tried more than 3 layers, the 4th layer is spaced as bad as the 3rd layer.
Here is my graph file:
digraph G {
nodesep=1.25;
splines=false;
node[width=1, shape=circle];
edge[style=invis];
subgraph cluster_1 {
label="Layer 1";
"1-1" -> "1-2" -> "1-3";
}
subgraph cluster_2 {
label="Layer 2";
"2-1" -> "2-2" -> "2-3";
}
subgraph cluster_3 {
label="Layer 3";
"3-1" -> "3-2" -> "3-3";
}
edge[style=solid, penwidth=1, constraint=false];
"1-1" -> "2-1";
"1-3" -> "2-1";
"1-1" -> "2-2";
"1-2" -> "2-2";
"1-2" -> "2-3";
"1-3" -> "2-3";
"2-1" -> "3-1";
"2-3" -> "3-1";
"2-1" -> "3-2";
"2-2" -> "3-2";
"2-2" -> "3-3";
"2-3" -> "3-3";
}
How can I go about getting my spacing symmetrical? Any help would be much appreciated. Thanks.
Update:
I have managed to get the spacing even, but it is not a perfect solution.
By placing an invisible node with invisible edges above the graph and connecting it to the top node in each layer, the layers space evenly. However, this node messes up spacing for things that need to be added above the image shown. So, is there a better way to do this?
Adding an Outer Cluster
Bounding box of outer cluster shown for clarity
Nesting the clusters cluster_1, cluster_2, and cluster_3 inside another cluster causes the layout engine to space them evenly.
Working With the Layout Engine
However, the bottom to top rankdir reverses the left to right display ordering to (cluster_3, cluster_2, cluster_1). Reversing the order in the source file fixes [kludges over] that.
Working Code
digraph G {
nodesep=1.25;
splines=false;
clusterrank=local;
node[width=1, shape=circle];
edge[style=invis];
subgraph cluster_0 {
subgraph cluster_3 {
label="Layer 3";
"3-1" -> "3-2" -> "3-3";
}
subgraph cluster_2 {
label="Layer 2";
"2-1" -> "2-2" -> "2-3";
}
subgraph cluster_1 {
label="Layer 1";
"1-1" -> "1-2" -> "1-3";
}
}
edge[style=solid, penwidth=1, constraint=false];
"1-1" -> "2-1";
"1-3" -> "2-1";
"1-1" -> "2-2";
"1-2" -> "2-2";
"1-2" -> "2-3";
"1-3" -> "2-3";
"2-1" -> {"3-1" "3-2"};
"2-3" -> {"3-1" "3-3"};
"2-2" -> {"3-2" "3-3"};
}
Notes
The new outer cluster can be styled so that it's bounding box is not visible.