From 3368e8917e9308517511cb2778317a1edfd5032c Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Thu, 21 Jul 2022 17:20:53 -0500
Subject: [PATCH 01/18] Improve Readme and docstring -distinguish args, kwargs
-add missing kwargs
---
README.md | 45 ++++++++++++++++++++++++------------
src/plot.jl | 66 ++++++++++++++++++++++++++++++-----------------------
2 files changed, 68 insertions(+), 43 deletions(-)
diff --git a/README.md b/README.md
index 63d836a..f5438ca 100644
--- a/README.md
+++ b/README.md
@@ -133,8 +133,8 @@ gplot(g, linetype="curve")
```
## Save to figure
-```{execute="false"}
-using Cairo, Compose
+```julia
+using Compose
# save to pdf
draw(PDF("karate.pdf", 16cm, 16cm), gplot(g))
# save to png
@@ -150,19 +150,34 @@ gplot(h)
```
# Arguments
-+ `G` graph to plot
-+ `layout` Optional. layout algorithm. Currently can choose from
-[random_layout, circular_layout, spring_layout, stressmajorize_layout,
-shell_layout, spectral_layout].
-Default: `spring_layout`
-+ `nodelabel` Optional. Labels for the vertices. Default: `nothing`
-+ `nodefillc` Optional. Color to fill the nodes with.
-Default: `colorant"turquoise"`
-+ `nodestrokec` Color for the node stroke.
-Default: `nothing`
-+ `arrowlengthfrac` Fraction of line length to use for arrows.
-Set to 0 for no arrows. Default: 0 for undirected graph and 0.1 for directed graph
-+ `arrowangleoffset` angular width in radians for the arrows. Default: `π/9` (20 degrees)
++ `G` Graph to draw
++ `locs_x, locs_y` Locations of the nodes (will be normalized and centered). If not specified, will be obtained from `layout` kwarg.
+
+# Keyword Arguments
++ `layout` Layout algorithm: `random_layout`, `circular_layout`, `spring_layout`, `shell_layout`, `stressmajorize_layout`, `spectral_layout`. Default: `spring_layout`
++ `NODESIZE` Max size for the nodes. Default: `3.0/sqrt(N)`
++ `nodesize` Relative size for the nodes, can be a Vector. Default: `1.0`
++ `nodelabel` Labels for the vertices, a Vector or nothing. Default: `nothing`
++ `nodelabelc` Color for the node labels, can be a Vector. Default: `colorant"black"`
++ `nodelabeldist` Distances for the node labels from center of nodes. Default: `0.0`
++ `nodelabelangleoffset` Angle offset for the node labels. Default: `π/4.0`
++ `NODELABELSIZE` Largest fontsize for the vertice labels. Default: `4.0`
++ `nodelabelsize` Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
++ `nodefillc` Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
++ `nodestrokec` Color for the nodes stroke, can be a Vector. Default: `nothing`
++ `nodestrokelw` Line width for the nodes stroke, can be a Vector. Default: `0.0`
++ `edgelabel` Labels for the edges, a Vector or nothing. Default: `[]`
++ `edgelabelc` Color for the edge labels, can be a Vector. Default: `colorant"black"`
++ `edgelabeldistx, edgelabeldisty` Distance for the edge label from center of edge. Default: `0.0`
++ `EDGELABELSIZE` Largest fontsize for the edge labels. Default: `4.0`
++ `edgelabelsize` Relative fontsize for the edge labels, can be a Vector. Default: `1.0`
++ `EDGELINEWIDTH` Max line width for the edges. Default: `0.25/sqrt(N)`
++ `edgelinewidth` Relative line width for the edges, can be a Vector. Default: `1.0`
++ `edgestrokec` Color for the edge strokes, can be a Vector. Default: `colorant"lightgray"`
++ `arrowlengthfrac` Fraction of line length to use for arrows. Equal to 0 for undirected graphs. Default: `0.1` for the directed graphs
++ `arrowangleoffset` Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
++ `linetype` Type of line used for edges ("straight", "curve"). Default: "straight"
++ `outangle` Angular width in radians for the edges (only used if `linetype = "curve`). Default: `π/5 (36 degrees)`
# Reporting Bugs
diff --git a/src/plot.jl b/src/plot.jl
index b38554c..8c4c033 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -10,79 +10,89 @@ a Compose tree of the graph layout
`G`
Graph to draw
+`locs_x, locs_y`
+Locations of the nodes. Can be any units you want,
+but will be normalized and centered anyway. If not provided, will
+be obtained from `layout` kwarg.
+
+**Keyword Arguments**
+
`layout`
-Optional. Layout algorithm. Currently can be one of [`random_layout`,
+Layout algorithm. Currently can be one of [`random_layout`,
`circular_layout`, `spring_layout`, `shell_layout`, `stressmajorize_layout`,
`spectral_layout`].
Default: `spring_layout`
-`locs_x, locs_y`
-Locations of the nodes. Can be any units you want,
-but will be normalized and centered anyway
-
`NODESIZE`
-Optional. Max size for the nodes. Default: `3.0/sqrt(N)`
+Max size for the nodes. Default: `3.0/sqrt(N)`
`nodesize`
-Optional. Relative size for the nodes, can be a Vector. Default: `1.0`
+Relative size for the nodes, can be a Vector. Default: `1.0`
`nodelabel`
-Optional. Labels for the vertices, a Vector or nothing. Default: `nothing`
+Labels for the vertices, a Vector or nothing. Default: `nothing`
`nodelabelc`
-Optional. Color for the node labels, can be a Vector. Default: `colorant"black"`
+Color for the node labels, can be a Vector. Default: `colorant"black"`
`nodelabeldist`
-Optional. Distances for the node labels from center of nodes. Default: `0.0`
+Distances for the node labels from center of nodes. Default: `0.0`
`nodelabelangleoffset`
-Optional. Angle offset for the node labels. Default: `π/4.0`
+Angle offset for the node labels. Default: `π/4.0`
`NODELABELSIZE`
-Optional. Largest fontsize for the vertice labels. Default: `4.0`
+Largest fontsize for the vertice labels. Default: `4.0`
`nodelabelsize`
-Optional. Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
+Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
`nodefillc`
-Optional. Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
+Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
`nodestrokec`
-Optional. Color for the nodes stroke, can be a Vector. Default: `nothing`
+Color for the nodes stroke, can be a Vector. Default: `nothing`
`nodestrokelw`
-Optional. Line width for the nodes stroke, can be a Vector. Default: `0.0`
+Line width for the nodes stroke, can be a Vector. Default: `0.0`
`edgelabel`
-Optional. Labels for the edges, a Vector or nothing. Default: `[]`
+Labels for the edges, a Vector or nothing. Default: `[]`
`edgelabelc`
-Optional. Color for the edge labels, can be a Vector. Default: `colorant"black"`
+Color for the edge labels, can be a Vector. Default: `colorant"black"`
`edgelabeldistx, edgelabeldisty`
-Optional. Distance for the edge label from center of edge. Default: `0.0`
+Distance for the edge label from center of edge. Default: `0.0`
`EDGELABELSIZE`
-Optional. Largest fontsize for the edge labels. Default: `4.0`
+Largest fontsize for the edge labels. Default: `4.0`
`edgelabelsize`
-Optional. Relative fontsize for the edge labels, can be a Vector. Default: `1.0`
+Relative fontsize for the edge labels, can be a Vector. Default: `1.0`
`EDGELINEWIDTH`
-Optional. Max line width for the edges. Default: `0.25/sqrt(N)`
+Max line width for the edges. Default: `0.25/sqrt(N)`
`edgelinewidth`
-Optional. Relative line width for the edges, can be a Vector. Default: `1.0`
+Relative line width for the edges, can be a Vector. Default: `1.0`
`edgestrokec`
-Optional. Color for the edge strokes, can be a Vector. Default: `colorant"lightgray"`
+Color for the edge strokes, can be a Vector. Default: `colorant"lightgray"`
`arrowlengthfrac`
-Optional. Fraction of line length to use for arrows.
+Fraction of line length to use for arrows.
Equal to 0 for undirected graphs. Default: `0.1` for the directed graphs
`arrowangleoffset`
-Optional. Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
+Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
+
+`linetype`
+Type of line used for edges ("straight", "curve"). Default: "straight"
+
+`outangle`
+Angular width in radians for the edges (only used if `linetype = "curve`).
+Default: `π/5 (36 degrees)`
"""
function gplot(g::AbstractGraph{T},
@@ -108,9 +118,9 @@ function gplot(g::AbstractGraph{T},
nodestrokec = nothing,
nodestrokelw = 0.0,
arrowlengthfrac = is_directed(g) ? 0.1 : 0.0,
- arrowangleoffset = π / 9.0,
+ arrowangleoffset = π / 9,
linetype = "straight",
- outangle = pi/5) where {T <:Integer, R <: Real}
+ outangle = π / 5) where {T <:Integer, R <: Real}
length(locs_x_in) != length(locs_y_in) && error("Vectors must be same length")
N = nv(g)
From febb53bf5f587a7ec12a7bd4663564f27d21f4e4 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Thu, 21 Jul 2022 17:44:03 -0500
Subject: [PATCH 02/18] fix #166
clarify that Cairo is required to visualize in vscode
---
README.md | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/README.md b/README.md
index f5438ca..e385cee 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ Other layout algorithms are wrapped from [NetworkX](https://github.com/networkx/
# Getting Started
From the Julia REPL the latest version can be installed with
-```{execute="false"}
+```julia
Pkg.add("GraphPlot")
```
GraphPlot is then loaded with
@@ -132,6 +132,10 @@ gplot(g, locs_x, locs_y, nodelabel=nodelabel)
gplot(g, linetype="curve")
```
+## Show plot
+
+When using an IDE such as VSCode, `Cairo.jl` is required to visualize the plot inside the IDE.
+
## Save to figure
```julia
using Compose
From 9bffdd99d381ee4cec8c2b9702a9ed029a856d87 Mon Sep 17 00:00:00 2001
From: Hector Perez <hperez16@gmail.com>
Date: Thu, 21 Jul 2022 18:02:52 -0500
Subject: [PATCH 03/18] Fix #175 to enable plotting to html
Checking for System OS was outdated
---
src/plot.jl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/plot.jl b/src/plot.jl
index 8c4c033..362ac90 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -241,11 +241,11 @@ end
# take from [Gadfly.jl](https://github.com/dcjones/Gadfly.jl)
function open_file(filename)
- if Sys.KERNEL == :Darwin
+ if Sys.isapple(Sys.KERNEL) #apple
run(`open $(filename)`)
- elseif Sys.KERNEL == :Linux || Sys.KERNEL == :FreeBSD
+ elseif Sys.islinux(Sys.KERNEL) || Sys.isbsd(Sys.KERNEL) #linux
run(`xdg-open $(filename)`)
- elseif Sys.KERNEL == :Windows
+ elseif Sys.iswindows(Sys.KERNEL) #windows
run(`$(ENV["COMSPEC"]) /c start $(filename)`)
else
@warn("Showing plots is not supported on OS $(string(Sys.KERNEL))")
From 080a1a474edff73a4e9a034c8f90290045b0a20a Mon Sep 17 00:00:00 2001
From: Hector Perez <hperez16@gmail.com>
Date: Thu, 21 Jul 2022 18:03:59 -0500
Subject: [PATCH 04/18] Document the use of gplothtml in README
---
README.md | 1 +
1 file changed, 1 insertion(+)
diff --git a/README.md b/README.md
index e385cee..e5dd530 100644
--- a/README.md
+++ b/README.md
@@ -135,6 +135,7 @@ gplot(g, linetype="curve")
## Show plot
When using an IDE such as VSCode, `Cairo.jl` is required to visualize the plot inside the IDE.
+When using the REPL, `gplothtml` will allow displaying the plot on a browser.
## Save to figure
```julia
From 3d32d077c5d3bf73a497dddbca9700b4eca8c014 Mon Sep 17 00:00:00 2001
From: Hector Perez <hperez16@gmail.com>
Date: Thu, 21 Jul 2022 18:08:05 -0500
Subject: [PATCH 05/18] Update open_file
Now matches gadfly.jl (https://github.com/GiovineItalia/Gadfly.jl/blob/master/src/open_file.jl)
---
src/plot.jl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/plot.jl b/src/plot.jl
index 362ac90..505f9b6 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -241,11 +241,11 @@ end
# take from [Gadfly.jl](https://github.com/dcjones/Gadfly.jl)
function open_file(filename)
- if Sys.isapple(Sys.KERNEL) #apple
+ if Sys.isapple() #apple
run(`open $(filename)`)
- elseif Sys.islinux(Sys.KERNEL) || Sys.isbsd(Sys.KERNEL) #linux
+ elseif Sys.islinux() || Sys.isbsd() #linux
run(`xdg-open $(filename)`)
- elseif Sys.iswindows(Sys.KERNEL) #windows
+ elseif Sys.iswindows() #windows
run(`$(ENV["COMSPEC"]) /c start $(filename)`)
else
@warn("Showing plots is not supported on OS $(string(Sys.KERNEL))")
From 2c64095c0aee95cbb220224ab8022f1be0209e2f Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Mon, 25 Jul 2022 16:22:21 -0500
Subject: [PATCH 06/18] Minor changes: -allow gplothtml to accept same
arguments as gplot -allow x/y-locs to be of different type (<: Real)
---
src/plot.jl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/plot.jl b/src/plot.jl
index 505f9b6..af438b7 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -96,7 +96,7 @@ Default: `π/5 (36 degrees)`
"""
function gplot(g::AbstractGraph{T},
- locs_x_in::Vector{R}, locs_y_in::Vector{R};
+ locs_x_in::Vector{R1}, locs_y_in::Vector{R2};
nodelabel = nothing,
nodelabelc = colorant"black",
nodelabelsize = 1.0,
@@ -120,7 +120,7 @@ function gplot(g::AbstractGraph{T},
arrowlengthfrac = is_directed(g) ? 0.1 : 0.0,
arrowangleoffset = π / 9,
linetype = "straight",
- outangle = π / 5) where {T <:Integer, R <: Real}
+ outangle = π / 5) where {T <:Integer, R1 <: Real, R2 <: Real}
length(locs_x_in) != length(locs_y_in) && error("Vectors must be same length")
N = nv(g)
@@ -253,13 +253,13 @@ function open_file(filename)
end
# taken from [Gadfly.jl](https://github.com/dcjones/Gadfly.jl)
-function gplothtml(g; layout::Function=spring_layout, keyargs...)
+function gplothtml(args...; keyargs...)
filename = string(tempname(), ".html")
output = open(filename, "w")
plot_output = IOBuffer()
draw(SVGJS(plot_output, Compose.default_graphic_width,
- Compose.default_graphic_width, false), gplot(g, layout(g)...; keyargs...))
+ Compose.default_graphic_width, false), gplot(args...; keyargs...))
plotsvg = String(take!(plot_output))
write(output,
From 222fb26a44cabc046779cf7d74bd5680ba7b2c65 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Mon, 25 Jul 2022 23:26:46 -0500
Subject: [PATCH 07/18] add TagBot to repo
---
.github/workflows/tagbot.yml | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
create mode 100644 .github/workflows/tagbot.yml
diff --git a/.github/workflows/tagbot.yml b/.github/workflows/tagbot.yml
new file mode 100644
index 0000000..32a9dd8
--- /dev/null
+++ b/.github/workflows/tagbot.yml
@@ -0,0 +1,20 @@
+name: TagBot
+on:
+ issue_comment:
+ types:
+ - created
+ workflow_dispatch:
+ inputs:
+ lookback:
+ default: 3
+permissions:
+ contents: write
+jobs:
+ TagBot:
+ if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+ runs-on: ubuntu-latest
+ steps:
+ - uses: JuliaRegistries/TagBot@v1
+ with:
+ token: ${{ secrets.GITHUB_TOKEN }}
+ ssh: ${{ secrets.DOCUMENTER_KEY }}
\ No newline at end of file
From 14d62b4d3c829dbc0c3fdfd3ffd5897b0e48ee42 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Tue, 26 Jul 2022 11:59:01 -0500
Subject: [PATCH 08/18] Fix #172. set background color (`backgroundc` kwarg):
and minor changes to plots.jl update README
---
README.md | 1 +
src/plot.jl | 30 +++++++++++++++++-------------
2 files changed, 18 insertions(+), 13 deletions(-)
diff --git a/README.md b/README.md
index e5dd530..0ea4643 100644
--- a/README.md
+++ b/README.md
@@ -183,6 +183,7 @@ gplot(h)
+ `arrowangleoffset` Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
+ `linetype` Type of line used for edges ("straight", "curve"). Default: "straight"
+ `outangle` Angular width in radians for the edges (only used if `linetype = "curve`). Default: `π/5 (36 degrees)`
++ `backgroundc` Color for the plot background. Default: `nothing`
# Reporting Bugs
diff --git a/src/plot.jl b/src/plot.jl
index af438b7..58b0bc6 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -42,10 +42,10 @@ Distances for the node labels from center of nodes. Default: `0.0`
Angle offset for the node labels. Default: `π/4.0`
`NODELABELSIZE`
-Largest fontsize for the vertice labels. Default: `4.0`
+Largest fontsize for the vertex labels. Default: `4.0`
`nodelabelsize`
-Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
+Relative fontsize for the vertex labels, can be a Vector. Default: `1.0`
`nodefillc`
Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
@@ -94,6 +94,9 @@ Type of line used for edges ("straight", "curve"). Default: "straight"
Angular width in radians for the edges (only used if `linetype = "curve`).
Default: `π/5 (36 degrees)`
+`backgroundc`
+Color for the plot background. Default: `nothing`
+
"""
function gplot(g::AbstractGraph{T},
locs_x_in::Vector{R1}, locs_y_in::Vector{R2};
@@ -120,7 +123,8 @@ function gplot(g::AbstractGraph{T},
arrowlengthfrac = is_directed(g) ? 0.1 : 0.0,
arrowangleoffset = π / 9,
linetype = "straight",
- outangle = π / 5) where {T <:Integer, R1 <: Real, R2 <: Real}
+ outangle = π / 5,
+ backgroundc = nothing) where {T <:Integer, R1 <: Real, R2 <: Real}
length(locs_x_in) != length(locs_y_in) && error("Vectors must be same length")
N = nv(g)
@@ -169,19 +173,19 @@ function gplot(g::AbstractGraph{T},
# Create nodes
nodecircle = fill(0.4Compose.w, length(locs_x))
if isa(nodesize, Real)
- for i = 1:length(locs_x)
- nodecircle[i] *= nodesize
- end
- else
- for i = 1:length(locs_x)
- nodecircle[i] *= nodesize[i]
- end
- end
+ for i = 1:length(locs_x)
+ nodecircle[i] *= nodesize
+ end
+ else
+ for i = 1:length(locs_x)
+ nodecircle[i] *= nodesize[i]
+ end
+ end
nodes = circle(locs_x, locs_y, nodecircle)
# Create node labels if provided
texts = nothing
- if nodelabel != nothing
+ if !isnothing(nodelabel)
text_locs_x = deepcopy(locs_x)
text_locs_y = deepcopy(locs_y)
texts = text(text_locs_x .+ nodesize .* (nodelabeldist * cos(nodelabelangleoffset)),
@@ -227,7 +231,7 @@ function gplot(g::AbstractGraph{T},
end
end
- compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
+ compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)), rectangle(-1.2, -1.2, +2.4, +2.4), fill(backgroundc),
compose(context(), texts, fill(nodelabelc), stroke(nothing), fontsize(nodelabelsize)),
compose(context(), nodes, fill(nodefillc), stroke(nodestrokec), linewidth(nodestrokelw)),
compose(context(), edgetexts, fill(edgelabelc), stroke(nothing), fontsize(edgelabelsize)),
From d610f151efbf4613591e2ca8c85fbd9d853d0bdd Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Tue, 26 Jul 2022 20:28:16 -0500
Subject: [PATCH 09/18] update arg syntax for gplot: (address #177)
-breaking change: linetype changed from String to Symbol
-breaking change: default for edgelabel is nothing (not []) to make consistent with nodelabel default
-remove all caps args
-improve some of the code in gplot (use isnothing, etc.)
---
README.md | 14 ++++-----
src/plot.jl | 76 +++++++++++++++++-------------------------------
test/runtests.jl | 4 +--
3 files changed, 35 insertions(+), 59 deletions(-)
diff --git a/README.md b/README.md
index 0ea4643..49c5313 100644
--- a/README.md
+++ b/README.md
@@ -129,7 +129,7 @@ gplot(g, locs_x, locs_y, nodelabel=nodelabel)
## Curve edge
```julia
-gplot(g, linetype="curve")
+gplot(g, linetype=:curve)
```
## Show plot
@@ -160,28 +160,28 @@ gplot(h)
# Keyword Arguments
+ `layout` Layout algorithm: `random_layout`, `circular_layout`, `spring_layout`, `shell_layout`, `stressmajorize_layout`, `spectral_layout`. Default: `spring_layout`
-+ `NODESIZE` Max size for the nodes. Default: `3.0/sqrt(N)`
++ `max_nodesize` Max size for the nodes. Default: `3.0/sqrt(N)`
+ `nodesize` Relative size for the nodes, can be a Vector. Default: `1.0`
+ `nodelabel` Labels for the vertices, a Vector or nothing. Default: `nothing`
+ `nodelabelc` Color for the node labels, can be a Vector. Default: `colorant"black"`
+ `nodelabeldist` Distances for the node labels from center of nodes. Default: `0.0`
+ `nodelabelangleoffset` Angle offset for the node labels. Default: `π/4.0`
-+ `NODELABELSIZE` Largest fontsize for the vertice labels. Default: `4.0`
++ `max_nodelabelsize` Largest fontsize for the vertice labels. Default: `4.0`
+ `nodelabelsize` Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
+ `nodefillc` Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
+ `nodestrokec` Color for the nodes stroke, can be a Vector. Default: `nothing`
+ `nodestrokelw` Line width for the nodes stroke, can be a Vector. Default: `0.0`
-+ `edgelabel` Labels for the edges, a Vector or nothing. Default: `[]`
++ `edgelabel` Labels for the edges, a Vector or nothing. Default: `nothing`
+ `edgelabelc` Color for the edge labels, can be a Vector. Default: `colorant"black"`
+ `edgelabeldistx, edgelabeldisty` Distance for the edge label from center of edge. Default: `0.0`
-+ `EDGELABELSIZE` Largest fontsize for the edge labels. Default: `4.0`
++ `max_edgelabelsize` Largest fontsize for the edge labels. Default: `4.0`
+ `edgelabelsize` Relative fontsize for the edge labels, can be a Vector. Default: `1.0`
-+ `EDGELINEWIDTH` Max line width for the edges. Default: `0.25/sqrt(N)`
++ `max_edgelinewidth` Max line width for the edges. Default: `0.25/sqrt(N)`
+ `edgelinewidth` Relative line width for the edges, can be a Vector. Default: `1.0`
+ `edgestrokec` Color for the edge strokes, can be a Vector. Default: `colorant"lightgray"`
+ `arrowlengthfrac` Fraction of line length to use for arrows. Equal to 0 for undirected graphs. Default: `0.1` for the directed graphs
+ `arrowangleoffset` Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
-+ `linetype` Type of line used for edges ("straight", "curve"). Default: "straight"
++ `linetype` Type of line used for edges (:straight, :curve). Default: :straight
+ `outangle` Angular width in radians for the edges (only used if `linetype = "curve`). Default: `π/5 (36 degrees)`
+ `backgroundc` Color for the plot background. Default: `nothing`
diff --git a/src/plot.jl b/src/plot.jl
index 58b0bc6..72c04bb 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -23,7 +23,7 @@ Layout algorithm. Currently can be one of [`random_layout`,
`spectral_layout`].
Default: `spring_layout`
-`NODESIZE`
+`max_nodesize`
Max size for the nodes. Default: `3.0/sqrt(N)`
`nodesize`
@@ -41,7 +41,7 @@ Distances for the node labels from center of nodes. Default: `0.0`
`nodelabelangleoffset`
Angle offset for the node labels. Default: `π/4.0`
-`NODELABELSIZE`
+`max_nodelabelsize`
Largest fontsize for the vertex labels. Default: `4.0`
`nodelabelsize`
@@ -57,7 +57,7 @@ Color for the nodes stroke, can be a Vector. Default: `nothing`
Line width for the nodes stroke, can be a Vector. Default: `0.0`
`edgelabel`
-Labels for the edges, a Vector or nothing. Default: `[]`
+Labels for the edges, a Vector or nothing. Default: `nothing`
`edgelabelc`
Color for the edge labels, can be a Vector. Default: `colorant"black"`
@@ -65,13 +65,13 @@ Color for the edge labels, can be a Vector. Default: `colorant"black"`
`edgelabeldistx, edgelabeldisty`
Distance for the edge label from center of edge. Default: `0.0`
-`EDGELABELSIZE`
+`max_edgelabelsize`
Largest fontsize for the edge labels. Default: `4.0`
`edgelabelsize`
Relative fontsize for the edge labels, can be a Vector. Default: `1.0`
-`EDGELINEWIDTH`
+`max_edgelinewidth`
Max line width for the edges. Default: `0.25/sqrt(N)`
`edgelinewidth`
@@ -88,7 +88,7 @@ Equal to 0 for undirected graphs. Default: `0.1` for the directed graphs
Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
`linetype`
-Type of line used for edges ("straight", "curve"). Default: "straight"
+Type of line used for edges (:straight, :curve). Default: :straight
`outangle`
Angular width in radians for the edges (only used if `linetype = "curve`).
@@ -103,38 +103,32 @@ function gplot(g::AbstractGraph{T},
nodelabel = nothing,
nodelabelc = colorant"black",
nodelabelsize = 1.0,
- NODELABELSIZE = 4.0,
+ max_nodelabelsize = 4.0,
nodelabeldist = 0.0,
nodelabelangleoffset = π / 4.0,
- edgelabel = [],
+ edgelabel = nothing,
edgelabelc = colorant"black",
edgelabelsize = 1.0,
- EDGELABELSIZE = 4.0,
+ max_edgelabelsize = 4.0,
edgestrokec = colorant"lightgray",
edgelinewidth = 1.0,
- EDGELINEWIDTH = 3.0 / sqrt(nv(g)),
+ max_edgelinewidth = 3.0 / sqrt(nv(g)),
edgelabeldistx = 0.0,
edgelabeldisty = 0.0,
nodesize = 1.0,
- NODESIZE = 0.25 / sqrt(nv(g)),
+ max_nodesize = 0.25 / sqrt(nv(g)),
nodefillc = colorant"turquoise",
nodestrokec = nothing,
nodestrokelw = 0.0,
arrowlengthfrac = is_directed(g) ? 0.1 : 0.0,
arrowangleoffset = π / 9,
- linetype = "straight",
+ linetype = :straight,
outangle = π / 5,
backgroundc = nothing) where {T <:Integer, R1 <: Real, R2 <: Real}
- length(locs_x_in) != length(locs_y_in) && error("Vectors must be same length")
- N = nv(g)
- NE = ne(g)
- if nodelabel != nothing && length(nodelabel) != N
- error("Must have one label per node (or none)")
- end
- if !isempty(edgelabel) && length(edgelabel) != NE
- error("Must have one label per edge (or none)")
- end
+ @assert length(locs_x_in) == length(locs_y_in) == nv(g) "Position vectors must be of the same length as the number of nodes"
+ @assert isnothing(nodelabel) || length(nodelabel) == nv(g) "`nodelabel` must either be `nothing` or a vector of the same length as the number of nodes"
+ @assert isnothing(edgelabel) || length(edgelabel) == ne(g) "`edgelabel` must either be `nothing` or a vector of the same length as the number of edges"
locs_x = Float64.(locs_x_in)
locs_y = Float64.(locs_y_in)
@@ -152,35 +146,18 @@ function gplot(g::AbstractGraph{T},
map!(z -> scaler(z, min_x, max_x), locs_x, locs_x)
map!(z -> scaler(z, min_y, max_y), locs_y, locs_y)
- # Determine sizes
- #NODESIZE = 0.25/sqrt(N)
- #LINEWIDTH = 3.0/sqrt(N)
-
- max_nodesize = NODESIZE / maximum(nodesize)
- nodesize *= max_nodesize
- max_edgelinewidth = EDGELINEWIDTH / maximum(edgelinewidth)
- edgelinewidth *= max_edgelinewidth
- max_edgelabelsize = EDGELABELSIZE / maximum(edgelabelsize)
- edgelabelsize *= max_edgelabelsize
- max_nodelabelsize = NODELABELSIZE / maximum(nodelabelsize)
- nodelabelsize *= max_nodelabelsize
+ # Scale sizes
+ nodesize *= (max_nodesize / maximum(nodesize))
+ edgelinewidth *= (max_edgelinewidth / maximum(edgelinewidth))
+ edgelabelsize *= (max_edgelabelsize / maximum(edgelabelsize))
+ nodelabelsize *= (max_nodelabelsize / maximum(nodelabelsize))
max_nodestrokelw = maximum(nodestrokelw)
if max_nodestrokelw > 0.0
- max_nodestrokelw = EDGELINEWIDTH / max_nodestrokelw
- nodestrokelw *= max_nodestrokelw
+ nodestrokelw *= (max_edgelinewidth / max_nodestrokelw)
end
# Create nodes
- nodecircle = fill(0.4Compose.w, length(locs_x))
- if isa(nodesize, Real)
- for i = 1:length(locs_x)
- nodecircle[i] *= nodesize
- end
- else
- for i = 1:length(locs_x)
- nodecircle[i] *= nodesize[i]
- end
- end
+ nodecircle = fill(0.4Compose.w, nv(g)) .* nodesize
nodes = circle(locs_x, locs_y, nodecircle)
# Create node labels if provided
@@ -194,7 +171,7 @@ function gplot(g::AbstractGraph{T},
end
# Create edge labels if provided
edgetexts = nothing
- if !isempty(edgelabel)
+ if !isnothing(edgelabel)
edge_locs_x = zeros(R, NE)
edge_locs_y = zeros(R, NE)
for (e_idx, e) in enumerate(edges(g))
@@ -202,16 +179,15 @@ function gplot(g::AbstractGraph{T},
j = dst(e)
mid_x = (locs_x[i]+locs_x[j]) / 2.0
mid_y = (locs_y[i]+locs_y[j]) / 2.0
- edge_locs_x[e_idx] = (is_directed(g) ? (mid_x+locs_x[j]) / 2.0 : mid_x) + edgelabeldistx * NODESIZE
- edge_locs_y[e_idx] = (is_directed(g) ? (mid_y+locs_y[j]) / 2.0 : mid_y) + edgelabeldisty * NODESIZE
-
+ edge_locs_x[e_idx] = (is_directed(g) ? (mid_x+locs_x[j]) / 2.0 : mid_x) + edgelabeldistx * max_nodesize
+ edge_locs_y[e_idx] = (is_directed(g) ? (mid_y+locs_y[j]) / 2.0 : mid_y) + edgelabeldisty * max_nodesize
end
edgetexts = text(edge_locs_x, edge_locs_y, map(string, edgelabel), [hcenter], [vcenter])
end
# Create lines and arrow heads
lines, arrows = nothing, nothing
- if linetype == "curve"
+ if linetype == :curve
if arrowlengthfrac > 0.0
curves_cord, arrows_cord = graphcurve(g, locs_x, locs_y, nodesize, arrowlengthfrac, arrowangleoffset, outangle)
lines = curve(curves_cord[:,1], curves_cord[:,2], curves_cord[:,3], curves_cord[:,4])
diff --git a/test/runtests.jl b/test/runtests.jl
index f38f8d6..4014ed5 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -93,7 +93,7 @@ end
add_edge!(g2, 1,2)
add_edge!(g2, 2,1)
- plot_and_save1(fname) = plot_and_save(fname, g2, linetype="curve")
+ plot_and_save1(fname) = plot_and_save(fname, g2, linetype=:curve)
refimg1 = joinpath(datadir, "curve.png")
@test test_images(VisualTest(plot_and_save1, refimg1), popup=!istravis) |> save_comparison |> success
@@ -102,7 +102,7 @@ end
add_edge!(g3, 1,2)
add_edge!(g3, 2,1)
- plot_and_save2(fname) = plot_and_save(fname, g3, linetype="curve")
+ plot_and_save2(fname) = plot_and_save(fname, g3, linetype=:curve)
refimg2 = joinpath(datadir, "self_directed.png")
@test test_images(VisualTest(plot_and_save2, refimg2), popup=!istravis) |> save_comparison |> success
From 5bc0ba37deb92dc0a10a1eca37946577c01a437d Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Wed, 27 Jul 2022 00:32:11 -0500
Subject: [PATCH 10/18] clarify docstring fix background color
---
README.md | 2 +-
src/plot.jl | 9 +++++----
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index 49c5313..58ada52 100644
--- a/README.md
+++ b/README.md
@@ -165,7 +165,7 @@ gplot(h)
+ `nodelabel` Labels for the vertices, a Vector or nothing. Default: `nothing`
+ `nodelabelc` Color for the node labels, can be a Vector. Default: `colorant"black"`
+ `nodelabeldist` Distances for the node labels from center of nodes. Default: `0.0`
-+ `nodelabelangleoffset` Angle offset for the node labels. Default: `π/4.0`
++ `nodelabelangleoffset` Angle offset for the node labels (only used when `nodelabeldist` is not zero). Default: `π/4.0`
+ `max_nodelabelsize` Largest fontsize for the vertice labels. Default: `4.0`
+ `nodelabelsize` Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
+ `nodefillc` Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
diff --git a/src/plot.jl b/src/plot.jl
index 72c04bb..d8e6248 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -39,7 +39,7 @@ Color for the node labels, can be a Vector. Default: `colorant"black"`
Distances for the node labels from center of nodes. Default: `0.0`
`nodelabelangleoffset`
-Angle offset for the node labels. Default: `π/4.0`
+Angle offset for the node labels (only used when `nodelabeldist` is not zero). Default: `π/4.0`
`max_nodelabelsize`
Largest fontsize for the vertex labels. Default: `4.0`
@@ -188,7 +188,7 @@ function gplot(g::AbstractGraph{T},
# Create lines and arrow heads
lines, arrows = nothing, nothing
if linetype == :curve
- if arrowlengthfrac > 0.0
+ if !iszero(arrowlengthfrac)
curves_cord, arrows_cord = graphcurve(g, locs_x, locs_y, nodesize, arrowlengthfrac, arrowangleoffset, outangle)
lines = curve(curves_cord[:,1], curves_cord[:,2], curves_cord[:,3], curves_cord[:,4])
arrows = line(arrows_cord)
@@ -197,7 +197,7 @@ function gplot(g::AbstractGraph{T},
lines = curve(curves_cord[:,1], curves_cord[:,2], curves_cord[:,3], curves_cord[:,4])
end
else
- if arrowlengthfrac > 0.0
+ if !iszero(arrowlengthfrac)
lines_cord, arrows_cord = graphline(g, locs_x, locs_y, nodesize, arrowlengthfrac, arrowangleoffset)
lines = line(lines_cord)
arrows = line(arrows_cord)
@@ -207,7 +207,8 @@ function gplot(g::AbstractGraph{T},
end
end
- compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)), rectangle(-1.2, -1.2, +2.4, +2.4), fill(backgroundc),
+ compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
+ compose(context(), rectangle(-1.2, -1.2, +2.4, +2.4), fill(backgroundc)),
compose(context(), texts, fill(nodelabelc), stroke(nothing), fontsize(nodelabelsize)),
compose(context(), nodes, fill(nodefillc), stroke(nodestrokec), linewidth(nodestrokelw)),
compose(context(), edgetexts, fill(edgelabelc), stroke(nothing), fontsize(edgelabelsize)),
From ef373d5b4ddfa83bb751f12ba1dd9939aa7611df Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Wed, 27 Jul 2022 01:52:30 -0500
Subject: [PATCH 11/18] minor changes: -use `iszero` -remove `stroke(nothing)`
or `fill(nothing` as `nothing` is already the default for these functions in
Compose.jl
---
src/plot.jl | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/plot.jl b/src/plot.jl
index d8e6248..1df938b 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -152,7 +152,7 @@ function gplot(g::AbstractGraph{T},
edgelabelsize *= (max_edgelabelsize / maximum(edgelabelsize))
nodelabelsize *= (max_nodelabelsize / maximum(nodelabelsize))
max_nodestrokelw = maximum(nodestrokelw)
- if max_nodestrokelw > 0.0
+ if !iszero(max_nodestrokelw)
nodestrokelw *= (max_edgelinewidth / max_nodestrokelw)
end
@@ -207,13 +207,14 @@ function gplot(g::AbstractGraph{T},
end
end
+ #build plot
compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
compose(context(), rectangle(-1.2, -1.2, +2.4, +2.4), fill(backgroundc)),
- compose(context(), texts, fill(nodelabelc), stroke(nothing), fontsize(nodelabelsize)),
+ compose(context(), texts, fill(nodelabelc), fontsize(nodelabelsize)),
compose(context(), nodes, fill(nodefillc), stroke(nodestrokec), linewidth(nodestrokelw)),
- compose(context(), edgetexts, fill(edgelabelc), stroke(nothing), fontsize(edgelabelsize)),
+ compose(context(), edgetexts, fill(edgelabelc), fontsize(edgelabelsize)),
compose(context(), arrows, stroke(edgestrokec), linewidth(edgelinewidth)),
- compose(context(), lines, stroke(edgestrokec), fill(nothing), linewidth(edgelinewidth)))
+ compose(context(), lines, stroke(edgestrokec), linewidth(edgelinewidth)))
end
function gplot(g; layout::Function=spring_layout, keyargs...)
From 4d574e0d95d838dc2c78275396043ee7157a304d Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Wed, 27 Jul 2022 09:16:46 -0500
Subject: [PATCH 12/18] clean up repo: -move layouts to layouts.jl -add
community_layout to readme -remove deprecations -remove shape.jl and
pienode.jl (not used anywhere)
---
README.md | 15 ++-
src/GraphPlot.jl | 5 -
src/collapse_plot.jl | 96 ---------------
src/deprecations.jl | 106 ----------------
src/layout.jl | 287 ++++++++++++++++++++++++++++++++++++++++++-
src/pienode.jl | 41 -------
src/plot.jl | 2 +-
src/shape.jl | 9 --
src/stress.jl | 175 --------------------------
9 files changed, 301 insertions(+), 435 deletions(-)
delete mode 100644 src/collapse_plot.jl
delete mode 100644 src/deprecations.jl
delete mode 100644 src/pienode.jl
delete mode 100644 src/shape.jl
delete mode 100644 src/stress.jl
diff --git a/README.md b/README.md
index 58ada52..f012ea5 100644
--- a/README.md
+++ b/README.md
@@ -127,6 +127,19 @@ locs_x, locs_y = shell_layout(g, nlist)
gplot(g, locs_x, locs_y, nodelabel=nodelabel)
```
+### stress majorize layout
+```julia
+gplot(g, layout=stressmajorize_layout)
+```
+
+### community layout
+```julia
+community_id = rand(1:3, nv(g)) #membership for each node
+node_c = [colorant"red",colorant"yellow",colorant"blue"] #colors for each community
+locs_x, locs_y = community_layout(g,community_id)
+gplot(g, locs_x, locs_y, nodefillc = node_c[community_id])
+```
+
## Curve edge
```julia
gplot(g, linetype=:curve)
@@ -159,7 +172,7 @@ gplot(h)
+ `locs_x, locs_y` Locations of the nodes (will be normalized and centered). If not specified, will be obtained from `layout` kwarg.
# Keyword Arguments
-+ `layout` Layout algorithm: `random_layout`, `circular_layout`, `spring_layout`, `shell_layout`, `stressmajorize_layout`, `spectral_layout`. Default: `spring_layout`
++ `layout` Layout algorithm: `random_layout`, `circular_layout`, `spring_layout`, `shell_layout`, `stressmajorize_layout`, `spectral_layout`, `community_layout`. Default: `spring_layout`
+ `max_nodesize` Max size for the nodes. Default: `3.0/sqrt(N)`
+ `nodesize` Relative size for the nodes, can be a Vector. Default: `1.0`
+ `nodelabel` Labels for the vertices, a Vector or nothing. Default: `nothing`
diff --git a/src/GraphPlot.jl b/src/GraphPlot.jl
index c1738c1..3472fb8 100644
--- a/src/GraphPlot.jl
+++ b/src/GraphPlot.jl
@@ -17,16 +17,11 @@ export
shell_layout,
stressmajorize_layout
-include("deprecations.jl")
-
# layout algorithms
include("layout.jl")
-include("stress.jl")
# ploting utilities
-include("shape.jl")
include("lines.jl")
include("plot.jl")
-include("collapse_plot.jl")
end # module
diff --git a/src/collapse_plot.jl b/src/collapse_plot.jl
deleted file mode 100644
index 2e1e062..0000000
--- a/src/collapse_plot.jl
+++ /dev/null
@@ -1,96 +0,0 @@
-using GraphPlot
-
-function collapse_graph(g::AbstractGraph, membership::Vector{Int})
- nb_comm = maximum(membership)
-
- collapsed_edge_weights = Vector{Dict{Int,Float64}}(undef, nb_comm)
- for i=1:nb_comm
- collapsed_edge_weights[i] = Dict{Int,Float64}()
- end
-
- for e in edges(g)
- u = src(e)
- v = dst(e)
- u_comm = membership[u]
- v_comm = membership[v]
-
- # for special case of undirected network
- if !is_directed(g)
- u_comm, v_comm = minmax(u_comm, v_comm)
- end
-
- if haskey(collapsed_edge_weights[u_comm], v_comm)
- collapsed_edge_weights[u_comm][v_comm] += 1
- else
- collapsed_edge_weights[u_comm][v_comm] = 1
- end
- end
-
- collapsed_graph = SimpleGraph(nb_comm)
- collapsed_weights = Float64[]
-
- for u=1:nb_comm
- for (v,w) in collapsed_edge_weights[u]
- add_edge!(collapsed_graph, u, v)
- push!(collapsed_weights, w)
- end
- end
-
- return collapsed_graph, collapsed_weights
-end
-
-function community_layout(g::AbstractGraph, membership::Vector{Int})
- N = length(membership)
- lx = zeros(N)
- ly = zeros(N)
- comms = Dict{Int,Vector{Int}}()
- for (idx,lbl) in enumerate(membership)
- if haskey(comms, lbl)
- push!(comms[lbl], idx)
- else
- comms[lbl] = Int[idx]
- end
- end
- h, w = collapse_graph(g, membership)
- clx, cly = spring_layout(h)
- for (lbl, nodes) in comms
- θ = range(0, stop=2pi, length=(length(nodes) + 1))[1:end-1]
- for (idx, node) in enumerate(nodes)
- lx[node] = 1.8*length(nodes)/N*cos(θ[idx]) + clx[lbl]
- ly[node] = 1.8*length(nodes)/N*sin(θ[idx]) + cly[lbl]
- end
- end
- return lx, ly
-end
-
-function collapse_layout(g::AbstractGraph, membership::Vector{Int})
- sg = Graphs.SimpleGraph(nv(g))
- for e in edges(g)
- u = src(e)
- v = dst(e)
- Graphs.add_edge!(sg, u, v)
- end
- N = length(membership)
- lx = zeros(N)
- ly = zeros(N)
- comms = Dict{Int,Vector{Int}}()
- for (idx,lbl) in enumerate(membership)
- if haskey(comms, lbl)
- push!(comms[lbl], idx)
- else
- comms[lbl] = Int[idx]
- end
- end
- h, w = collapse_graph(g, membership)
- clx, cly = spring_layout(h)
- for (lbl, nodes) in comms
- subg = sg[nodes]
- sublx, subly = spring_layout(subg)
- θ = range(0, stop=2pi, length=(length(nodes) + 1))[1:end-1]
- for (idx, node) in enumerate(nodes)
- lx[node] = 1.8*length(nodes)/N*sublx[idx] + clx[lbl]
- ly[node] = 1.8*length(nodes)/N*subly[idx] + cly[lbl]
- end
- end
- return lx, ly
-end
diff --git a/src/deprecations.jl b/src/deprecations.jl
deleted file mode 100644
index 4e07ac3..0000000
--- a/src/deprecations.jl
+++ /dev/null
@@ -1,106 +0,0 @@
-using Base: depwarn
-
-
-function _nv(g)
- depwarn("`GraphPlot._nv(g)` is deprectated. Use `Graphs.nv(g)` instead.", :_nv)
- return Graphs.nv(g)
-end
-
-function _ne(g)
- depwarn("`GraphPlot._ne(g)` is deprectated. Use `Graphs.ne(g)` instead.", :_ne)
- return Graphs.ne(g)
-end
-
-function _vertices(g)
- depwarn("`GraphPlot._vertices(g)` is deprectated. Use `Graphs.vertices(g)` instead.", :_vertices)
- return Graphs.vertices(g)
-end
-
-function _edges(g)
- depwarn("`GraphPlot._edges(g)` is deprectated. Use `Graphs.edges(g)` instead.", :_edges)
- return Graphs.edges(g)
-end
-
-function _src_index(e, g)
- depwarn("`GraphPlot._src_index(g)` is deprectated. Use `Graphs.src(e)` instead.", :_src_index)
- return Graphs.src(e)
-end
-
-function _dst_index(e, g)
- depwarn("`GraphPlot._dst_index(g)` is deprectated. Use `Graphs.dst(e)` instead.", :_dst_index)
- return Graphs.dst(e)
-end
-
-function _adjacency_matrix(g)
- depwarn("`GraphPlot._adjacency_matrix(g)` is deprectated. Use `Graphs.adjacency_matrix(g)` instead.", :_adjacency_matrix)
- return Graphs.adjacency_matrix(g)
-end
-
-function _is_directed(g)
- depwarn("`GraphPlot._is_directed(g)` is deprectated. Use `Graphs.is_directed(g)` instead.", :_is_directed)
- return Graphs.is_directed(g)
-end
-
-function _laplacian_matrix(g)
- depwarn("`GraphPlot._laplacian_matrix(g)` is deprectated. Use `Graphs.laplacian_matrix(g)` instead.", :_laplacian_matrix)
- return Graphs.laplacian_matrix(g)
-end
-
-
-"""
-read some famous graphs
-
-**Paramenters**
-
-*graphname*
-Currently, `graphname` can be one of ["karate", "football", "dolphins",
-"netscience", "polbooks", "power", "cond-mat"]
-
-**Return**
-a graph
-
-**Example**
- julia> g = graphfamous("karate")
-"""
-function graphfamous(graphname::AbstractString)
- depwarn("""
- `graphfamous` has been deprecated and will be removed in the future. Consider the package `GraphIO.jl` for loading graphs.
- """, :graphfamous)
- file = joinpath(dirname(@__DIR__), "data", graphname*".dat")
- readedgelist(file)
-end
-export graphfamous
-
-using DelimitedFiles: readdlm
-"""read graph from in edgelist format"""
-function readedgelist(filename; is_directed::Bool=false, start_index::Int=0, delim::Char=' ')
- depwarn("""
- `graphfamous` has been deprecated and will be removed in the future. Consider the package `GraphIO.jl` for loading graphs.
- """, :graphfamous)
- es = readdlm(filename, delim, Int)
- es = unique(es, dims=1)
- if start_index == 0
- es = es .+ 1
- end
- N = maximum(es)
- if is_directed
- g = DiGraph(N)
- for i=1:size(es,1)
- add_edge!(g, es[i,1], es[i,2])
- end
- return g
- else
- for i=1:size(es,1)
- if es[i,1] > es[i,2]
- es[i,1], es[i,2] = es[i,2], es[i,1]
- end
- end
- es = unique(es, dims=1)
- g = Graph(N)
- for i=1:size(es,1)
- add_edge!(g, es[i,1], es[i,2])
- end
- return g
- end
-end
-export readedgelist
diff --git a/src/layout.jl b/src/layout.jl
index 2a9956b..5507b89 100644
--- a/src/layout.jl
+++ b/src/layout.jl
@@ -1,7 +1,7 @@
using SparseArrays: SparseMatrixCSC, sparse
using ArnoldiMethod: SR
using Base: OneTo
-using LinearAlgebra: eigen
+using LinearAlgebra: eigen, norm
"""
Position nodes uniformly at random in the unit square.
@@ -284,3 +284,288 @@ function _spectral(A::SparseMatrixCSC)
index = sortperm(real(eigenvalues))[2:3]
return real(eigenvectors[:, index[1]]), real(eigenvectors[:, index[2]])
end
+
+# This layout algorithm is copy from [IainNZ](https://github.com/IainNZ)'s [GraphLayout.jl](https://github.com/IainNZ/GraphLayout.jl)
+@doc """
+Compute graph layout using stress majorization
+
+Inputs:
+
+ δ: Matrix of pairwise distances
+ p: Dimension of embedding (default: 2)
+ w: Matrix of weights. If not specified, defaults to
+ w[i,j] = δ[i,j]^-2 if δ[i,j] is nonzero, or 0 otherwise
+ X0: Initial guess for the layout. Coordinates are given in rows.
+ If not specified, default to random matrix of Gaussians
+
+Additional optional keyword arguments control the convergence of the algorithm
+and the additional output as requested:
+
+ maxiter: Maximum number of iterations. Default: 400size(X0, 1)^2
+ abstols: Absolute tolerance for convergence of stress.
+ The iterations terminate if the difference between two
+ successive stresses is less than abstol.
+ Default: √(eps(eltype(X0))
+ reltols: Relative tolerance for convergence of stress.
+ The iterations terminate if the difference between two
+ successive stresses relative to the current stress is less than
+ reltol. Default: √(eps(eltype(X0))
+ abstolx: Absolute tolerance for convergence of layout.
+ The iterations terminate if the Frobenius norm of two successive
+ layouts is less than abstolx. Default: √(eps(eltype(X0))
+ verbose: If true, prints convergence information at each iteration.
+ Default: false
+ returnall: If true, returns all iterates and their associated stresses.
+ If false (default), returns the last iterate
+
+Output:
+
+ The final layout X, with coordinates given in rows, unless returnall=true.
+
+Reference:
+
+ The main equation to solve is (8) of:
+
+ @incollection{
+ author = {Emden R Gansner and Yehuda Koren and Stephen North},
+ title = {Graph Drawing by Stress Majorization}
+ year={2005},
+ isbn={978-3-540-24528-5},
+ booktitle={Graph Drawing},
+ seriesvolume={3383},
+ series={Lecture Notes in Computer Science},
+ editor={Pach, J\'anos},
+ doi={10.1007/978-3-540-31843-9_25},
+ publisher={Springer Berlin Heidelberg},
+ pages={239--250},
+ }
+"""
+function stressmajorize_layout(g::AbstractGraph,
+ p::Int=2,
+ w=nothing,
+ X0=randn(nv(g), p);
+ maxiter = 400size(X0, 1)^2,
+ abstols=√(eps(eltype(X0))),
+ reltols=√(eps(eltype(X0))),
+ abstolx=√(eps(eltype(X0))),
+ verbose = false)
+
+ @assert size(X0, 2)==p
+ δ = fill(1.0, nv(g), nv(g))
+
+ if w == nothing
+ w = δ.^-2
+ w[.!isfinite.(w)] .= 0
+ end
+
+ @assert size(X0, 1)==size(δ, 1)==size(δ, 2)==size(w, 1)==size(w, 2)
+ Lw = weightedlaplacian(w)
+ pinvLw = pinv(Lw)
+ newstress = stress(X0, δ, w)
+ Xs = Matrix[X0]
+ stresses = [newstress]
+ iter = 0
+ for outer iter = 1:maxiter
+ #TODO the faster way is to drop the first row and col from the iteration
+ X = pinvLw * (LZ(X0, δ, w)*X0)
+ @assert all(isfinite.(X))
+ newstress, oldstress = stress(X, δ, w), newstress
+ verbose && @info("""Iteration $iter
+ Change in coordinates: $(norm(X - X0))
+ Stress: $newstress (change: $(newstress-oldstress))
+ """)
+ push!(Xs, X)
+ push!(stresses, newstress)
+ abs(newstress - oldstress) < reltols * newstress && break
+ abs(newstress - oldstress) < abstols && break
+ norm(X - X0) < abstolx && break
+ X0 = X
+ end
+ iter == maxiter && @warn("Maximum number of iterations reached without convergence")
+
+ Xs[end][:,1], Xs[end][:,2]
+end
+
+@doc """
+Stress function to majorize
+
+Input:
+ X: A particular layout (coordinates in rows)
+ d: Matrix of pairwise distances
+ w: Weights for each pairwise distance
+
+See (1) of Reference
+"""
+function stress(X, d=fill(1.0, size(X, 1), size(X, 1)), w=nothing)
+ s = 0.0
+ n = size(X, 1)
+ if w==nothing
+ w = d.^-2
+ w[!isfinite.(w)] = 0
+ end
+ @assert n==size(d, 1)==size(d, 2)==size(w, 1)==size(w, 2)
+ for j=1:n, i=1:j-1
+ s += w[i, j] * (norm(X[i,:] - X[j,:]) - d[i,j])^2
+ end
+ @assert isfinite(s)
+ return s
+end
+
+@doc """
+Compute weighted Laplacian given ideal weights w
+
+Lʷ defined in (4) of the Reference
+"""
+function weightedlaplacian(w)
+ n = LinearAlgebra.checksquare(w)
+ T = eltype(w)
+ Lw = zeros(T, n, n)
+ for i=1:n
+ D = zero(T)
+ for j=1:n
+ i==j && continue
+ Lw[i, j] = -w[i, j]
+ D += w[i, j]
+ end
+ Lw[i, i] = D
+ end
+ return Lw
+end
+
+@doc """
+Computes L^Z defined in (5) of the Reference
+
+Input: Z: current layout (coordinates)
+ d: Ideal distances (default: all 1)
+ w: weights (default: d.^-2)
+"""
+function LZ(Z, d, w)
+ n = size(Z, 1)
+ L = zeros(n, n)
+ for i=1:n
+ D = 0.0
+ for j=1:n
+ i==j && continue
+ nrmz = norm(Z[i,:] - Z[j,:])
+ nrmz==0 && continue
+ δ = w[i, j] * d[i, j]
+ L[i, j] = -δ/nrmz
+ D -= -δ/nrmz
+ end
+ L[i, i] = D
+ end
+ @assert all(isfinite.(L))
+ L
+end
+
+"""
+Community layout for graphs with pre-defined community assignments
+
+**Parameters**
+
+*g*
+a graph
+
+*membership*
+`Vector` indicating the membership (`Int`) of each node
+
+**Examples**
+```
+julia> g = smallgraph(:karate)
+julia> member_id = rand(1:5, nv(g))
+julia> locs_x, locs_y = spectral_layout(g, member_id)
+```
+"""
+function community_layout(g::AbstractGraph, membership::Vector{Int}=collect(vertices(g)))
+ N = length(membership)
+ lx = zeros(N)
+ ly = zeros(N)
+ comms = Dict{Int,Vector{Int}}()
+ for (idx,lbl) in enumerate(membership)
+ if haskey(comms, lbl)
+ push!(comms[lbl], idx)
+ else
+ comms[lbl] = Int[idx]
+ end
+ end
+ h = collapse_graph(g, membership)[1]
+ clx, cly = spring_layout(h)
+ for (lbl, nodes) in comms
+ θ = range(0, stop=2pi, length=(length(nodes) + 1))[1:end-1]
+ for (idx, node) in enumerate(nodes)
+ lx[node] = 1.8*length(nodes)/N*cos(θ[idx]) + clx[lbl]
+ ly[node] = 1.8*length(nodes)/N*sin(θ[idx]) + cly[lbl]
+ end
+ end
+ return lx, ly
+end
+
+function collapse_layout(g::AbstractGraph, membership::Vector{Int})
+ sg = Graphs.SimpleGraph(nv(g))
+ for e in edges(g)
+ u = src(e)
+ v = dst(e)
+ Graphs.add_edge!(sg, u, v)
+ end
+ N = length(membership)
+ lx = zeros(N)
+ ly = zeros(N)
+ comms = Dict{Int,Vector{Int}}()
+ for (idx,lbl) in enumerate(membership)
+ if haskey(comms, lbl)
+ push!(comms[lbl], idx)
+ else
+ comms[lbl] = Int[idx]
+ end
+ end
+ h = collapse_graph(g, membership)[1]
+ clx, cly = spring_layout(h)
+ for (lbl, nodes) in comms
+ subg = sg[nodes]
+ sublx, subly = spring_layout(subg)
+ for (idx, node) in enumerate(nodes)
+ lx[node] = 1.8*length(nodes)/N*sublx[idx] + clx[lbl]
+ ly[node] = 1.8*length(nodes)/N*subly[idx] + cly[lbl]
+ end
+ end
+ return lx, ly
+end
+
+function collapse_graph(g::AbstractGraph, membership::Vector{Int})
+ nb_comm = maximum(membership)
+
+ collapsed_edge_weights = Vector{Dict{Int,Float64}}(undef, nb_comm)
+ for i=1:nb_comm
+ collapsed_edge_weights[i] = Dict{Int,Float64}()
+ end
+
+ for e in edges(g)
+ u = src(e)
+ v = dst(e)
+ u_comm = membership[u]
+ v_comm = membership[v]
+
+ # for special case of undirected network
+ if !is_directed(g)
+ u_comm, v_comm = minmax(u_comm, v_comm)
+ end
+
+ if haskey(collapsed_edge_weights[u_comm], v_comm)
+ collapsed_edge_weights[u_comm][v_comm] += 1
+ else
+ collapsed_edge_weights[u_comm][v_comm] = 1
+ end
+ end
+
+ collapsed_graph = SimpleGraph(nb_comm)
+ collapsed_weights = Float64[]
+
+ for u=1:nb_comm
+ for (v,w) in collapsed_edge_weights[u]
+ add_edge!(collapsed_graph, u, v)
+ push!(collapsed_weights, w)
+ end
+ end
+
+ return collapsed_graph, collapsed_weights
+end
\ No newline at end of file
diff --git a/src/pienode.jl b/src/pienode.jl
deleted file mode 100644
index dbafe5b..0000000
--- a/src/pienode.jl
+++ /dev/null
@@ -1,41 +0,0 @@
-# to do
-mutable struct PIENODE
- x::Float64
- y::Float64
- r::Float64
- prop::Vector{Float64}
- colors
- strokes
-end
-
-function pie(pn::PIENODE)
- p = [0.0;2pi*pn.prop/sum(pn.prop)]
- θ = cumsum(p)
- s = Vector[]
- for i=1:length(θ)-1
- push!(s, sector(pn.x, pn.y, pn.r, θ[i], θ[i+1]))
- end
- compose(context(),path(s), fill(pn.colors), stroke(pn.strokes))
-end
-
-function sector(x, y, r, θ1, θ2)
- if θ2-θ1<=pi
- [:M, x+r*cos(θ1),y-r*sin(θ1), :A, r, r, 0, false, false, x+r*cos(θ2), y-r*sin(θ2), :L, x, y, :Z]
- else
- [
- :M, x+r*cos(θ1),y-r*sin(θ1),
- :A, r, r, 0, false, false, x+r*cos(θ1+pi), y-r*sin(θ1+pi),
- :A, r, r, 0, false, false, x+r*cos(θ2), y-r*sin(θ2),
- :L, x, y,
- :Z
- ]
- end
-end
-
-function sector(x::Vector{T}, y::Vector{T}, r::Vector{T}, θ1::Vector{T}, θ2::Vector{T}) where {T}
- s = Vector[]
- for i=1:length(x)
- push!(s, sector(x[i],y[i],r[i],θ1[i],θ2[i]))
- end
- s
-end
diff --git a/src/plot.jl b/src/plot.jl
index 1df938b..7b0d36d 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -20,7 +20,7 @@ be obtained from `layout` kwarg.
`layout`
Layout algorithm. Currently can be one of [`random_layout`,
`circular_layout`, `spring_layout`, `shell_layout`, `stressmajorize_layout`,
-`spectral_layout`].
+`spectral_layout`, `community_layout`].
Default: `spring_layout`
`max_nodesize`
diff --git a/src/shape.jl b/src/shape.jl
deleted file mode 100644
index a3e6549..0000000
--- a/src/shape.jl
+++ /dev/null
@@ -1,9 +0,0 @@
-# draw a regular n-gon
-function ngon(x, y, r, n=3, θ=0.0)
- αs = linspace(0,2pi,n+1)[1:end-1]
- [(r*cos(α-θ)+x, r*sin(α-θ)+y) for α in αs]
-end
-
-function ngon(xs::Vector, ys::Vector, rs::Vector, ns::Vector=fill(3,length(xs)), θs::Vector=zeros(length(xs)))
- [ngon(xs[i], ys[i], rs[i], ns[i], θs[i]) for i=1:length(xs)]
-end
diff --git a/src/stress.jl b/src/stress.jl
deleted file mode 100644
index f09c708..0000000
--- a/src/stress.jl
+++ /dev/null
@@ -1,175 +0,0 @@
-using LinearAlgebra
-
-# This layout algorithm is copy from [IainNZ](https://github.com/IainNZ)'s [GraphLayout.jl](https://github.com/IainNZ/GraphLayout.jl)
-@doc """
-Compute graph layout using stress majorization
-
-Inputs:
-
- δ: Matrix of pairwise distances
- p: Dimension of embedding (default: 2)
- w: Matrix of weights. If not specified, defaults to
- w[i,j] = δ[i,j]^-2 if δ[i,j] is nonzero, or 0 otherwise
- X0: Initial guess for the layout. Coordinates are given in rows.
- If not specified, default to random matrix of Gaussians
-
-Additional optional keyword arguments control the convergence of the algorithm
-and the additional output as requested:
-
- maxiter: Maximum number of iterations. Default: 400size(X0, 1)^2
- abstols: Absolute tolerance for convergence of stress.
- The iterations terminate if the difference between two
- successive stresses is less than abstol.
- Default: √(eps(eltype(X0))
- reltols: Relative tolerance for convergence of stress.
- The iterations terminate if the difference between two
- successive stresses relative to the current stress is less than
- reltol. Default: √(eps(eltype(X0))
- abstolx: Absolute tolerance for convergence of layout.
- The iterations terminate if the Frobenius norm of two successive
- layouts is less than abstolx. Default: √(eps(eltype(X0))
- verbose: If true, prints convergence information at each iteration.
- Default: false
- returnall: If true, returns all iterates and their associated stresses.
- If false (default), returns the last iterate
-
-Output:
-
- The final layout X, with coordinates given in rows, unless returnall=true.
-
-Reference:
-
- The main equation to solve is (8) of:
-
- @incollection{
- author = {Emden R Gansner and Yehuda Koren and Stephen North},
- title = {Graph Drawing by Stress Majorization}
- year={2005},
- isbn={978-3-540-24528-5},
- booktitle={Graph Drawing},
- seriesvolume={3383},
- series={Lecture Notes in Computer Science},
- editor={Pach, J\'anos},
- doi={10.1007/978-3-540-31843-9_25},
- publisher={Springer Berlin Heidelberg},
- pages={239--250},
- }
-"""
-function stressmajorize_layout(g::AbstractGraph,
- p::Int=2,
- w=nothing,
- X0=randn(nv(g), p);
- maxiter = 400size(X0, 1)^2,
- abstols=√(eps(eltype(X0))),
- reltols=√(eps(eltype(X0))),
- abstolx=√(eps(eltype(X0))),
- verbose = false,
- returnall = false)
-
- @assert size(X0, 2)==p
- δ = fill(1.0, nv(g), nv(g))
-
- if w == nothing
- w = δ.^-2
- w[.!isfinite.(w)] .= 0
- end
-
- @assert size(X0, 1)==size(δ, 1)==size(δ, 2)==size(w, 1)==size(w, 2)
- Lw = weightedlaplacian(w)
- pinvLw = pinv(Lw)
- newstress = stress(X0, δ, w)
- Xs = Matrix[X0]
- stresses = [newstress]
- iter = 0
- for outer iter = 1:maxiter
- #TODO the faster way is to drop the first row and col from the iteration
- X = pinvLw * (LZ(X0, δ, w)*X0)
- @assert all(isfinite.(X))
- newstress, oldstress = stress(X, δ, w), newstress
- verbose && @info("""Iteration $iter
- Change in coordinates: $(norm(X - X0))
- Stress: $newstress (change: $(newstress-oldstress))
- """)
- push!(Xs, X)
- push!(stresses, newstress)
- abs(newstress - oldstress) < reltols * newstress && break
- abs(newstress - oldstress) < abstols && break
- norm(X - X0) < abstolx && break
- X0 = X
- end
- iter == maxiter && @warn("Maximum number of iterations reached without convergence")
- #returnall ? (Xs, stresses) : Xs[end]
- Xs[end][:,1], Xs[end][:,2]
-end
-
-@doc """
-Stress function to majorize
-
-Input:
- X: A particular layout (coordinates in rows)
- d: Matrix of pairwise distances
- w: Weights for each pairwise distance
-
-See (1) of Reference
-"""
-function stress(X, d=fill(1.0, size(X, 1), size(X, 1)), w=nothing)
- s = 0.0
- n = size(X, 1)
- if w==nothing
- w = d.^-2
- w[!isfinite.(w)] = 0
- end
- @assert n==size(d, 1)==size(d, 2)==size(w, 1)==size(w, 2)
- for j=1:n, i=1:j-1
- s += w[i, j] * (norm(X[i,:] - X[j,:]) - d[i,j])^2
- end
- @assert isfinite(s)
- return s
-end
-
-@doc """
-Compute weighted Laplacian given ideal weights w
-
-Lʷ defined in (4) of the Reference
-"""
-function weightedlaplacian(w)
- n = LinearAlgebra.checksquare(w)
- T = eltype(w)
- Lw = zeros(T, n, n)
- for i=1:n
- D = zero(T)
- for j=1:n
- i==j && continue
- Lw[i, j] = -w[i, j]
- D += w[i, j]
- end
- Lw[i, i] = D
- end
- return Lw
-end
-
-@doc """
-Computes L^Z defined in (5) of the Reference
-
-Input: Z: current layout (coordinates)
- d: Ideal distances (default: all 1)
- w: weights (default: d.^-2)
-"""
-function LZ(Z, d, w)
- n = size(Z, 1)
- L = zeros(n, n)
- for i=1:n
- D = 0.0
- for j=1:n
- i==j && continue
- nrmz = norm(Z[i,:] - Z[j,:])
- nrmz==0 && continue
- δ = w[i, j] * d[i, j]
- L[i, j] = -δ/nrmz
- D -= -δ/nrmz
- end
- L[i, i] = D
- end
- @assert all(isfinite.(L))
- L
-end
From 67bd950938f19c6c00eb5a0ff659745c6a43a1b4 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Wed, 27 Jul 2022 09:50:55 -0500
Subject: [PATCH 13/18] Fix #154
Multiple dispatch was messing up because types were not specified for spring layout and `kws` not preceeded by `;`
---
src/layout.jl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/layout.jl b/src/layout.jl
index 5507b89..85320d1 100644
--- a/src/layout.jl
+++ b/src/layout.jl
@@ -102,11 +102,11 @@ julia> locs_x, locs_y = spring_layout(g)
```
"""
function spring_layout(g::AbstractGraph,
- locs_x=2*rand(nv(g)).-1.0,
- locs_y=2*rand(nv(g)).-1.0;
+ locs_x::Vector{R1}=2*rand(nv(g)).-1.0,
+ locs_y::Vector{R2}=2*rand(nv(g)).-1.0;
C=2.0,
MAXITER=100,
- INITTEMP=2.0)
+ INITTEMP=2.0) where {R1 <: Real, R2 <: Real}
nvg = nv(g)
adj_matrix = adjacency_matrix(g)
@@ -174,7 +174,7 @@ end
using Random: MersenneTwister
-function spring_layout(g::AbstractGraph, seed::Integer, kws...)
+function spring_layout(g::AbstractGraph, seed::Integer; kws...)
rng = MersenneTwister(seed)
spring_layout(g, 2 .* rand(rng, nv(g)) .- 1.0, 2 .* rand(rng,nv(g)) .- 1.0; kws...)
end
From 22cddebcea3c609631b0703effd64412dff79891 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Wed, 27 Jul 2022 10:37:05 -0500
Subject: [PATCH 14/18] make default consistent with gplot notation (pi/9)
---
src/lines.jl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/lines.jl b/src/lines.jl
index 4589641..8b1a857 100644
--- a/src/lines.jl
+++ b/src/lines.jl
@@ -180,7 +180,7 @@ function graphcurve(g::AbstractGraph{T}, locs_x, locs_y, nodesize::Vector{<:Real
end
# this function is copy from [IainNZ](https://github.com/IainNZ)'s [GraphLayout.jl](https://github.com/IainNZ/GraphLayout.jl)
-function arrowcoords(θ, endx, endy, arrowlength, angleoffset=20.0/180.0*π)
+function arrowcoords(θ, endx, endy, arrowlength, angleoffset=π/9)
arr1x = endx - arrowlength*cos(θ+angleoffset)
arr1y = endy - arrowlength*sin(θ+angleoffset)
arr2x = endx - arrowlength*cos(θ-angleoffset)
From 6f4597f5d3323016ae65de56efdcd9ecc1eafd93 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Tue, 2 Aug 2022 09:32:47 -0500
Subject: [PATCH 15/18] Revert "Fix #154"
This reverts commit 67bd950938f19c6c00eb5a0ff659745c6a43a1b4.
---
src/layout.jl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/layout.jl b/src/layout.jl
index 85320d1..5507b89 100644
--- a/src/layout.jl
+++ b/src/layout.jl
@@ -102,11 +102,11 @@ julia> locs_x, locs_y = spring_layout(g)
```
"""
function spring_layout(g::AbstractGraph,
- locs_x::Vector{R1}=2*rand(nv(g)).-1.0,
- locs_y::Vector{R2}=2*rand(nv(g)).-1.0;
+ locs_x=2*rand(nv(g)).-1.0,
+ locs_y=2*rand(nv(g)).-1.0;
C=2.0,
MAXITER=100,
- INITTEMP=2.0) where {R1 <: Real, R2 <: Real}
+ INITTEMP=2.0)
nvg = nv(g)
adj_matrix = adjacency_matrix(g)
@@ -174,7 +174,7 @@ end
using Random: MersenneTwister
-function spring_layout(g::AbstractGraph, seed::Integer; kws...)
+function spring_layout(g::AbstractGraph, seed::Integer, kws...)
rng = MersenneTwister(seed)
spring_layout(g, 2 .* rand(rng, nv(g)) .- 1.0, 2 .* rand(rng,nv(g)) .- 1.0; kws...)
end
From 40e21beec22dcc7128c36af2adae5082c0482f26 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Tue, 2 Aug 2022 09:33:34 -0500
Subject: [PATCH 16/18] Revert "bug fix"
Remove commits that are in separate PRs
This reverts commit d4a2ae4ba42a701ebe49865d2addf212c54f7bd7.
---
README.md | 1 -
src/plot.jl | 35 ++++++++++++++++++++++++++++++-----
2 files changed, 30 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index f012ea5..f34804c 100644
--- a/README.md
+++ b/README.md
@@ -196,7 +196,6 @@ gplot(h)
+ `arrowangleoffset` Angular width in radians for the arrows. Default: `π/9 (20 degrees)`
+ `linetype` Type of line used for edges (:straight, :curve). Default: :straight
+ `outangle` Angular width in radians for the edges (only used if `linetype = "curve`). Default: `π/5 (36 degrees)`
-+ `backgroundc` Color for the plot background. Default: `nothing`
# Reporting Bugs
diff --git a/src/plot.jl b/src/plot.jl
index 7b0d36d..c9d650d 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -41,11 +41,16 @@ Distances for the node labels from center of nodes. Default: `0.0`
`nodelabelangleoffset`
Angle offset for the node labels (only used when `nodelabeldist` is not zero). Default: `π/4.0`
+<<<<<<< HEAD
`max_nodelabelsize`
Largest fontsize for the vertex labels. Default: `4.0`
+=======
+`NODELABELSIZE`
+Largest fontsize for the vertice labels. Default: `4.0`
+>>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
`nodelabelsize`
-Relative fontsize for the vertex labels, can be a Vector. Default: `1.0`
+Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
`nodefillc`
Color to fill the nodes with, can be a Vector. Default: `colorant"turquoise"`
@@ -94,9 +99,6 @@ Type of line used for edges (:straight, :curve). Default: :straight
Angular width in radians for the edges (only used if `linetype = "curve`).
Default: `π/5 (36 degrees)`
-`backgroundc`
-Color for the plot background. Default: `nothing`
-
"""
function gplot(g::AbstractGraph{T},
locs_x_in::Vector{R1}, locs_y_in::Vector{R2};
@@ -122,9 +124,14 @@ function gplot(g::AbstractGraph{T},
nodestrokelw = 0.0,
arrowlengthfrac = is_directed(g) ? 0.1 : 0.0,
arrowangleoffset = π / 9,
+<<<<<<< HEAD
linetype = :straight,
outangle = π / 5,
backgroundc = nothing) where {T <:Integer, R1 <: Real, R2 <: Real}
+=======
+ linetype = "straight",
+ outangle = π / 5) where {T <:Integer, R1 <: Real, R2 <: Real}
+>>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
@assert length(locs_x_in) == length(locs_y_in) == nv(g) "Position vectors must be of the same length as the number of nodes"
@assert isnothing(nodelabel) || length(nodelabel) == nv(g) "`nodelabel` must either be `nothing` or a vector of the same length as the number of nodes"
@@ -157,12 +164,25 @@ function gplot(g::AbstractGraph{T},
end
# Create nodes
+<<<<<<< HEAD
nodecircle = fill(0.4Compose.w, nv(g)) .* nodesize
+=======
+ nodecircle = fill(0.4Compose.w, length(locs_x))
+ if isa(nodesize, Real)
+ for i = 1:length(locs_x)
+ nodecircle[i] *= nodesize
+ end
+ else
+ for i = 1:length(locs_x)
+ nodecircle[i] *= nodesize[i]
+ end
+ end
+>>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
nodes = circle(locs_x, locs_y, nodecircle)
# Create node labels if provided
texts = nothing
- if !isnothing(nodelabel)
+ if nodelabel != nothing
text_locs_x = deepcopy(locs_x)
text_locs_y = deepcopy(locs_y)
texts = text(text_locs_x .+ nodesize .* (nodelabeldist * cos(nodelabelangleoffset)),
@@ -207,10 +227,15 @@ function gplot(g::AbstractGraph{T},
end
end
+<<<<<<< HEAD
#build plot
compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
compose(context(), rectangle(-1.2, -1.2, +2.4, +2.4), fill(backgroundc)),
compose(context(), texts, fill(nodelabelc), fontsize(nodelabelsize)),
+=======
+ compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
+ compose(context(), texts, fill(nodelabelc), stroke(nothing), fontsize(nodelabelsize)),
+>>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
compose(context(), nodes, fill(nodefillc), stroke(nodestrokec), linewidth(nodestrokelw)),
compose(context(), edgetexts, fill(edgelabelc), fontsize(edgelabelsize)),
compose(context(), arrows, stroke(edgestrokec), linewidth(edgelinewidth)),
From f4f375f9b266ec34ff15de54653437220ff9e208 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Tue, 2 Aug 2022 09:47:06 -0500
Subject: [PATCH 17/18] Revert "bug fix"
Remove commits that are in separate PRs
This reverts commit d4a2ae4ba42a701ebe49865d2addf212c54f7bd7.
---
src/plot.jl | 29 -----------------------------
1 file changed, 29 deletions(-)
diff --git a/src/plot.jl b/src/plot.jl
index c9d650d..2107b8e 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -44,10 +44,6 @@ Angle offset for the node labels (only used when `nodelabeldist` is not zero). D
<<<<<<< HEAD
`max_nodelabelsize`
Largest fontsize for the vertex labels. Default: `4.0`
-=======
-`NODELABELSIZE`
-Largest fontsize for the vertice labels. Default: `4.0`
->>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
`nodelabelsize`
Relative fontsize for the vertice labels, can be a Vector. Default: `1.0`
@@ -124,14 +120,8 @@ function gplot(g::AbstractGraph{T},
nodestrokelw = 0.0,
arrowlengthfrac = is_directed(g) ? 0.1 : 0.0,
arrowangleoffset = π / 9,
-<<<<<<< HEAD
linetype = :straight,
- outangle = π / 5,
- backgroundc = nothing) where {T <:Integer, R1 <: Real, R2 <: Real}
-=======
- linetype = "straight",
outangle = π / 5) where {T <:Integer, R1 <: Real, R2 <: Real}
->>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
@assert length(locs_x_in) == length(locs_y_in) == nv(g) "Position vectors must be of the same length as the number of nodes"
@assert isnothing(nodelabel) || length(nodelabel) == nv(g) "`nodelabel` must either be `nothing` or a vector of the same length as the number of nodes"
@@ -164,20 +154,7 @@ function gplot(g::AbstractGraph{T},
end
# Create nodes
-<<<<<<< HEAD
nodecircle = fill(0.4Compose.w, nv(g)) .* nodesize
-=======
- nodecircle = fill(0.4Compose.w, length(locs_x))
- if isa(nodesize, Real)
- for i = 1:length(locs_x)
- nodecircle[i] *= nodesize
- end
- else
- for i = 1:length(locs_x)
- nodecircle[i] *= nodesize[i]
- end
- end
->>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
nodes = circle(locs_x, locs_y, nodecircle)
# Create node labels if provided
@@ -227,15 +204,9 @@ function gplot(g::AbstractGraph{T},
end
end
-<<<<<<< HEAD
#build plot
compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
- compose(context(), rectangle(-1.2, -1.2, +2.4, +2.4), fill(backgroundc)),
compose(context(), texts, fill(nodelabelc), fontsize(nodelabelsize)),
-=======
- compose(context(units=UnitBox(-1.2, -1.2, +2.4, +2.4)),
- compose(context(), texts, fill(nodelabelc), stroke(nothing), fontsize(nodelabelsize)),
->>>>>>> parent of 14d62b4 (Fix #172. set background color (`backgroundc` kwarg):)
compose(context(), nodes, fill(nodefillc), stroke(nodestrokec), linewidth(nodestrokelw)),
compose(context(), edgetexts, fill(edgelabelc), fontsize(edgelabelsize)),
compose(context(), arrows, stroke(edgestrokec), linewidth(edgelinewidth)),
From 1a945c4688930f2fb95eb9fba2f1378778ddbbf4 Mon Sep 17 00:00:00 2001
From: hdavid16 <hperez16@gmail.com>
Date: Tue, 2 Aug 2022 09:47:31 -0500
Subject: [PATCH 18/18] no change
.
---
src/plot.jl | 1 -
1 file changed, 1 deletion(-)
diff --git a/src/plot.jl b/src/plot.jl
index 2107b8e..fe6e553 100644
--- a/src/plot.jl
+++ b/src/plot.jl
@@ -41,7 +41,6 @@ Distances for the node labels from center of nodes. Default: `0.0`
`nodelabelangleoffset`
Angle offset for the node labels (only used when `nodelabeldist` is not zero). Default: `π/4.0`
-<<<<<<< HEAD
`max_nodelabelsize`
Largest fontsize for the vertex labels. Default: `4.0`