I wrote the below DOT to generate a diagram. In addition to the nodes that are defined and laid out, I want to place one node to the left and another node to the right of the edge marked L, they should be close to L and in between NODE3 and NODE6.
I tried with some invisible nodes. The new nodes either go to the first row or the second row, but I want them to be in the new row between the first and second.
digraph g {
ranksep=0.5
graph [rankdir = "TB"];
graph [splines=ortho];
node [fontsize = "8"];
edge [];
node0 [label = "{NODE0}" shape = "record" ];
node1 [label = "{NODE1}" shape = "record" ];
node2 [label = "{NODE2}" shape = "record" ];
node3 [label = "{NODE3}" shape = "record" ];
node4 [label = "{NODE4}" shape = "record" ];
node5 [label = "{NODE5}" shape = "record" ];
node6 [label = "{NODE6}" shape = "record" ];
node7 [label = "{NODE7}" shape = "record" ];
node8 [label = "{NODE8}" shape = "record" ];
node9 [label = "{NODE9}" shape = "record" ];
node10 [label = "{NODE10}" shape = "record" ];
node11 [label = "{NODE11}" shape = "record" ];
node12 [label = "{NODE12}" shape = "record" ];
{rank=same; node0 -> node1 -> node2 -> node3 -> node4};
{rank=same; node5 -> node6 -> node7 -> node8 -> node9};
{rank=same; node10 -> node11 -> node12};
node1 -> node5;
node5 -> node3;
node3 -> node6[label="L"];
node7 -> node10;
node11 -> node8;
node9 -> node12;
}
How about something like this? I created a "point" node for the new ones to connect to within their rank. Also fiddled with the arrowheads to give you an idea of the possibilities there.
digraph g {
ranksep=0.5
graph [rankdir = "TB"];
graph [splines=ortho];
node [fontsize = "8"];
edge [];
node0 [label = "{NODE0}" shape = "record" ];
node1 [label = "{NODE1}" shape = "record" ];
node2 [label = "{NODE2}" shape = "record" ];
node3 [label = "{NODE3}" shape = "record" ];
node4 [label = "{NODE4}" shape = "record" ];
node5 [label = "{NODE5}" shape = "record" ];
node6 [label = "{NODE6}" shape = "record" ];
node7 [label = "{NODE7}" shape = "record" ];
node8 [label = "{NODE8}" shape = "record" ];
node9 [label = "{NODE9}" shape = "record" ];
node10 [label = "{NODE10}" shape = "record" ];
node11 [label = "{NODE11}" shape = "record" ];
node12 [label = "{NODE12}" shape = "record" ];
nodenew1 [label="new1" shape=record];
nodenew2 [label="new2" shape=record];
{rank=same; node0 -> node1 -> node2 -> node3 -> node4};
{rank=same; node5 -> node6 -> node7 -> node8 -> node9};
{rank=same; node10 -> node11 -> node12};
node1 -> node5;
node5 -> node3;
{
rank = same;
nodenew1 -> nodepoint -> nodenew2 [ arrowhead=none]
}
nodepoint [shape=point]
node3 -> nodepoint [label="L" arrowhead=none];
nodepoint -> node6[label="L"];
node7 -> node10;
node11 -> node8;
node9 -> node12;
}
Related
I am using DiagrammeR/grViz in R Studio to make a flow chart from left to right. I have included the R code below. This works fine but I would like to align Block 1 to Block 6 with the top so that they are flush at the top.
Any ideas or links to help would be appreciated.
library(DiagrammeR)
grViz("
digraph boxes_and_circles {
graph[rankdir = LR]
graph [overlap = false, fontsize = 10]
node[shape = rectangle, style = filled, style = rounded]
subgraph cluster_0 {
label = 'BLOCK 1'
node [shape = box,
fixedsize = true,
height = 0.7,
width = 1.2,
]
CS1[label = '1A'];
CS2[label = '1B'];
CS3[label = '1C'];
}
subgraph cluster_1 {
label = 'BLOCK 2'
node [shape = circle,
fixedsize = true,
width = 1.2,
] // sets as circles
CR1[label = '2A'];
CR2[label = '2B'];
}
subgraph cluster_3 {
label = 'BLOCK 4'
node [shape = box,
fixedsize = true,
height = 0.7,
width = 1.2,
]
RM1; RM2;
RM1[label = '4A'];
RM2[label = '4B'];
}
subgraph cluster_5 {
label = 'BLOCK 6'
node [shape = box,
fixedsize = true,
height = 0.7,
width = 1.2,
]
R1[label = '6A'];
R2[label = '6B'];
R3[label = '6C'];
}
CS1->CR1->RM1->R1
CS1-> R1
CS2->CR2->RM2->R1
CS1->CR2
CS3-> R3
}
")
I found the following example of diagrammeR here (diagrammer - how can I add arms to my flowchart?):
library(DiagrammeR)
grViz("digraph flowchart {
# node definitions with substituted label text
node [fontname = Helvetica, shape = rectangle, fixedsize = false, width = 1]
1 [label = 'data (100%)']
2 [label = 'data (74.4%)']
3 [label = 'data (69.6%)']
4 [label = 'data (55.4%)']
m1 [label = 'missing (25.6%)']
m2 [label = 'missing (4.8%)']
node [shape=none, width=0, height=0, label='']
p1 -> 2; p2 -> 3 -> 4;
{rank=same; p1 -> m1}
{rank=same; p2 -> m2}
edge [dir=none]
1 -> p1; 2 -> p2;
}")
Output is:
In my case I have multiple exclusions (m2, m3, m4, m5, m6, m7, m8) between box 2 and 3:
grViz("digraph flowchart {
# node definitions with substituted label text
node [fontname = Helvetica, shape = rectangle, fixedsize = false, width = 1]
1 [label = 'Box 1']
2 [label = 'Box 2']
3 [label = 'Box 3']
m1 [label = 'm1']
m2 [label = 'm2']
m3 [label = 'm3']
m4 [label = 'm4']
m5 [label = 'm5']
m6 [label = 'm6']
m7 [label = 'm7']
m8 [label = 'm8']
node [shape=none, width=0, height=0, label='']
p1 -> 2; p2 -> 3;
{rank=same; p1 -> m1}
{rank=same; p2 -> m2}
{rank=same; p2 -> m3}
{rank=same; p2 -> m4}
{rank=same; p2 -> m5}
{rank=same; p2 -> m6}
{rank=same; p2 -> m7}
{rank=same; p2 -> m8}
edge [dir=none]
1 -> p1; 2 -> p2;
}")
Currently this gives me:
But I would like to have a longer arrow between box 2 and 3 so that all m boxes are one below the other, and not to the right, is this possible? Like:
Box 2
|--- m2
|--- m3
|--- m4
|--- m5
|--- m6
|--- m7
|--- m8
Box 3
This should get you up and running. Just add more (p3 -> p4... in edge section etc.).
library(DiagrammeR)
grViz("digraph flowchart {
# node definitions with substituted label text
node [fontname = Helvetica, shape = rectangle, fixedsize = false, width = 1]
1 [label = 'Box 1']
2 [label = 'Box 2']
3 [label = 'Box 3']
m1 [label = 'm1']
m2 [label = 'm2']
m3 [label = 'm3']
node [shape=none, width=0, height=0, label='']
p1 -> 2; p3 -> 3
{rank=same; p1 -> m1}
{rank=same; p2 -> m2}
{rank=same; p3 -> m3}
edge [dir=none, arrowhead=none]
1 -> p1; 2 -> p2; p2 -> p3
}")
I have noticed that I am getting errors in my footnote interpretations over the last week or so. I tried updating to the latest version as well as the latest github download. I have also updated R and R studio to the latest versions.
Starting with footnote 10, there is a misinterpretation of the previously outlined labels:
grViz("
digraph {
graph [layout = dot]
node [shape = box, fontname = Helvetica]
a [label = '##1']
b [label = '##2']
c [label = '##3']
d [label = '##4']
e [label = '##5']
f [label = '##6']
g [label = '##7']
h [label = '##8']
i [label = '##9']
j [label = '##10']
k [label = '##11']
l [label = '##12']
m [label = '##13']
n [label = '##14']
o [label = '##15']
p [label = '##16']
a -> {b c d}
b -> {e f}
c -> {g h}
d -> {i j}
e -> {k}
f -> {l}
g -> {m}
h -> {n}
i -> {o}
j -> {p}
}
[1]: 'hello'
[2]: 'there'
[3]: 'how'
[4]: 'are'
[5]: 'you'
[6]: 'today'
[7]: 7
[8]: 8
[9]: 9
[10]: 'this one is interpreted as ##1 + 0 rather than ##10'
[11]: 'this one is interpreted as ##1 + 1 rather than ##11'
[12]: 'etc'
[13]: 'etc'
[14]: 'etc'
[15]: 'etc'
[16]: 'etc'
")
This way of writing the substitution works. Each level in the diagram gets its own hyphenated series.
grViz("
digraph boxes_and_circles {
# several 'node' statements
node [shape = box, color = tomato,
fontname = Helvetica]
a ; b ; c1 ; c2 ; d1 ; d2 ; d3 ; d4 ; e1 ; e2 ; e3 ; e4 ; e5 ; e6 ; e7 ; e8
# 'edge' statements
a->b->{c1,c2} c1->{d1,d2} c2->{d3,d4} d1->{e1,e2} d2->{e3,e4} d3->{e5,e6} d4->{e7,e8}
# a 'graph' statement
graph [overlap = true, fontsize = 10]
a [label = 'Enrolled\nN=##1']
b [label = 'Randomized\nN=##2']
c1 [label = '15-Day\nN=##3-1']
c2 [label = '60-Day\nN=##3-2']
d1 [label = 'WGS\nPositive\nN=##4-1']
d2 [label = 'WGS\nNegative\nN=##4-2']
d3 [label = 'WGS\nPositive\nN=##4-3']
d4 [label = 'WGS\nNegative\nN=##4-4']
e1 [label = 'Visit3 COM\nTRUE\nN=##5-1']
e2 [label = 'Visit3 COM\nFALSE\nN=##5-2']
e3 [label = 'Visit3 COM\nTRUE\nN=##5-3']
e4 [label = 'Visit3 COM\nFALSE\nN=##5-4']
e5 [label = 'Visit3 COM\nTRUE\nN=##5-5']
e6 [label = 'Visit3 COM\nFALSE\nN=##5-6']
e7 [label = 'Visit3 COM\nTRUE\nN=##5-7']
e8 [label = 'Visit3 COM\nFALSE\nN=##5-8']
}
[1]: A
[2]: B
[3]: c(C1,C2)
[4]: c(D1,D2,D3,D4)
[5]: c(E1,E2,E3,E4,E5,E6,E7,E8)
")
Is it possible to reproduce a meta-analysis type of flowchart as the one in the picture below using any R tool?
My attempt was using mermaid:
diagram = "
graph LR
subgraph Screening
b1-->b2
end
subgraph Eligibility
c1-->c2
end
subgraph Included
d1-->d2
end
subgraph Identification
a1-->a2
end
"
mermaid(diagram)
Which generated:
But I cannot find a way of connect the nodes accross the subgraphs.
Is there another tool better fitting to this kind of job? I am thinking on any package that I could use from within my Rmarkdown document.
I have found the DiagrammeR package easiest to do this. The general idea would be something like:
library(glue)
library(DiagrammeR)
excluded <- glue('Full text articles excluded
n = 1000
Reasons for exclusion
Reason 1
Reason 2')
grViz("
digraph cohort_flow_chart
{
node [fontname = Helvetica, fontsize = 12, shape = box, width = 4]
a[label = 'Records identified in original search']
b[label = 'Records identified with update']
c[label = 'Records after duplicates removed']
d[label = 'Records screened']
e[label = 'Records excluded']
f[label = 'Full text articles assessed']
g[label = 'Studies included']
h[label = '##1']
{ rank = same; a b}
{ rank = same; d, e}
{ rank = same; f, h}
a -> c;
b -> c;
c -> d;
d -> e [ minlen = 3 ];
d -> f;
f -> h [ minlen = 3 ];
f -> g;
}
[1]: excluded
")
Will look like:
Image with labels and empty nodes
grViz("
digraph cohort_flow_chart
{
node [fontname = Helvetica, fontsize = 12, shape = box, width = 4]
i[label = 'Identification', fillcolor = LightBlue,
style = filled, width = 2]
j[label = 'Screening',fillcolor = LightBlue, style = filled, width = 2]
k[label = 'Eligibility', fillcolor = LightBlue, style = filled,
width = 2]
l[label = 'Included', fillcolor = LightBlue, style = filled, width = 2]
a[label = 'Records identified in original search']
b[label = 'Records identified with update']
c[label = 'Records after duplicates removed']
d[label = 'Records screened']
e[label = 'Records excluded']
f[label = 'Full text articles assessed']
g[label = 'Studies included']
h[label = '##1']
blank_1[label = '', width = 0.01, height = 0.01]
blank_2[label = '', width = 0.01, height = 0.01]
blank_4[label = '', width = 4, color = White]
{ rank = same; a b i}
{ rank = same; blank_4 c j}
{ rank = same; f k}
{ rank = same; g l}
{ rank = same; blank_1 e}
{ rank = same; blank_2 h}
a -> c;
b -> c;
b -> blank_4 [ dir = none, color = White];
c -> d;
d -> blank_1 [ dir = none ];
blank_1 -> e [ minlen = 3 ];
blank_1 -> f;
f -> blank_2 [ dir = none ];
blank_2 -> h [ minlen = 3 ];
blank_2 -> g;
}
[1]: excluded
")
I can't find out how to draw a curved line between two rectangle using graphviz such as
digraph G {
SatisfactionF [style=filled, shape = rectangle]
SatisfactionM [style=filled, shape = rectangle]
Marital[shape = circle]
SatisfactionF -> Marital
SatisfactionM -> Marital
}
Here you go:
digraph G {
{
rank = same;
SatisfactionF [style=filled, shape = rectangle]
SatisfactionM [style=filled, shape = rectangle]
}
Marital[shape = circle]
SatisfactionF -> Marital
SatisfactionM -> Marital
SatisfactionF -> SatisfactionM [label = "0.4" tailport=n headport=n dir=both arrowhead=none]
}
It gives a warning but it works.