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alph-0.4.1
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alph
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | alph-0.4.1 |
| نام | alph |
| نسخه کتابخانه | 0.4.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Uros Rapajic |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | https://github.com/connectedcompany/alph |
| آدرس اینترنتی | https://pypi.org/project/alph/ |
| مجوز | - |
# **alph** - <b>al</b>tair for your gra<b>ph</b>
A Python library using [Altair](https://altair-viz.github.io/) for declarative, data-driven network visualisation.
<p align="center"><img alt="Alph graph" src="examples/images/small_graph.png" width=60%/></p>
## Why
Tidy, legible graph visualisations can be elusive. Alph helps by bringing together effective styling, layout and pruning options from across the Python ecosystem.
## How it works
1. Get your data into a NetworkX Graph
2. Pick a network layout function, or bring your own node coordinates
3. Define node and edge style attributes
4. Plot using a simple function call
Best bet is probably to dive straight into the [examples](./examples/), and come back to the API documentation below as needed.
## Features
- plot any NetworkX Graph
- support for any layout expressed as a NetworkX `pos` structure (a dict like `{node_id: (x,y), ...}`)
- several readily accessible and tunable layout functions (see [example](examples/3_layouts_gallery.ipynb))
- Altair-style data driven node and edge styling - size, colour, stroke, opacity, scales, conditionals and more
- convenience args for node labels, halos
- experimental 1-level "combo" node support
## Installation
### Minimal
```
pip install alph
```
### Recommended
1. for graphviz layout support, install graphviz on your platform - e.g. `brew install graphviz` on Mac,
`sudo apt install graphviz` on Debian / Ubuntu etc - or [download the installer](https://graphviz.org/download/)
2. Install alph with graphviz support:
```
pip install alph[graphviz]
```
3. Install the ForceAtlas2 layout library from our fork, along with cython for speedup
```
pip install cython git+https://github.com/connectedcompany/forceatlas2.git
```
> #### Why is the ForceAtlas2 install separate?
>
> [ForceAtlas2](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098679) is a classic,
> user feedback led layout algorithm from the [Gephi](https://gephi.org/) team, and the [ForceAtlas2 library](https://github.com/bhargavchippada/forceatlas2)
> implementation is an excellent, performant Python port. There are two things to be aware of:
>
> 1. **GPL licence** - the ForceAtlas2 library, and some of the works it is derived from, are GPL licensed -
> hence care is needed when distributing and linking to it. We thus intend to keep its install optional
> long term. Since alph uses a plugin design for layout providers, this is straightforward for us to
> accommodate, and maintain explicit separation for use cases where GPL is an issue.
>
> 2. **Our fork** - recently, releases of the library have been sporradic - though there is stated intent for
> regular maintenance to resume. In the meantime, we've created a temporary fork to be able to roll in
> changes. Currently, our fork incorporates a simple change that enables deterministic layouts.
## Usage
Simply call the `alph` function with desired options.
Minimally, given a weighted network G:
```
from alph import alph
G = ...
alph(G, weight_attr="weight")
```
## Examples
See [`examples`](./examples). Here's a taster:
- Some of the supported layouts (from the [layouts gallery example](examples/3_layouts_gallery.ipynb)):
- Use of geolocation coordinates for graph layout, (from the [flight routes example](examples/5_flight_routes.ipynb)):
- A styled interaction network (from the [dolphins example](examples/4_dolphins.ipynb)):
- "Combo"-style layout (experimental) - category-driven node grouping with edge weight aggregation, from the [Les Mis example](examples/6_les_mis_experimental_combo.ipynb):
---
# API
### Supported layout functions
- [NetworkX layouts](https://networkx.org/documentation/stable/reference/drawing.html#module-networkx.drawing.layout): Spring, Fruchterman-Reingold, etc
- NetworkX-wrapped [graphviz layouts](https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_agraph.graphviz_layout.html):
dot, neato etc
- Gephi ForceAtlas2 based on the
[forceatlas2 Python implementation](https://github.com/bhargavchippada/forceatlas2) -
see [layout.py](./alph/layout.py) for configuration options, and
[this paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098679)
for more detail
- ForceAtlas implementation within [scikit-network](https://github.com/sknetwork-team/scikit-network)
- Any other that returns a NetworkX-style node positions dictionary
### Supported arguments
| arg | type(s) | default | description |
| -------------------------------- | ---------------------- | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| G | Networkx Graph | | graph to visualise |
| weight_attr | str | | edge weight attribute, for weighted graphs |
| layout_fn | function | ForceAtlas2 | Function that, given a graph, returns a layout |
| node args | dict | | See below |
| edge args | dict | | See below |
| combo_group_by | str or list | | Attribute to use to create grouped combo nodes |
| combo_layout_fn | function | Fruchterman-Reingold | Layout function for combo nodes |
| combo_node_args | dict | | See below |
| combo_edge_args | dict | | See below |
| combo_edge_weight_agg_attr | dict | | Attribute to use to weigh combo edges; if set, overrides weight_attr. Can use values given via combo_edge_agg_attrs. If not set and weight_attr not given, falls back to simple edge count. |
| combo_edge_agg_attrs | dict | | Pandas groupby-style dict, describing how to aggregate edge attributes that span nodes - for example `{"combo_edge_attr_name": ("edge_attr_name", "sum")}` |
| combo_edge_weight_threshold | dict | | Drop edges below this weight |
| include_edgeless_combo_nodes | dict | | Whether or not to incorporate disconnected combo nodes |
| combo_node_additional_attrs | dict | | Attributes to add to combo nodes |
| edge_node_additional_attrs | dict | | Attributes to add to combo node edges, like `{"edge_attr_name": agg_fn}`; agg fn is applied across all attr values for edges that link grouped nodes |
| combo_empty_attr_action | drop, group or promote | `drop` | What to do with nodes that have an empty value for the combo_group_by attribute |
| combo_size_scale_domain | 2-item list or tuple | `[0, 25]` | Lower/upper bound of num nodes to apply to combo node size range |
| combo_size_scale_range | 2-item list or tuple | `[6^2, 180^2]` | Combo node size range |
| combo_inner_graph_scale_factor | float | `0.6` | Scale down inner graph to fit inside combo nodes by this factor - normally <1 |
| non_serializable_datetime_format | str | `%d %b %Y` | Format string for non-serialisable date / time types that otherwise break Altair |
| width | int | `800` | Figure width (px) |
| height | int | `600` | Figure height (px) |
| prop_kwargs | dict | | Optional properties such as title |
| padding | int | | Padding inside figure edges. No node centres will be placed outside this boundary. |
### Node args
| arg | type(s) | default |
| ---------------- | ------------- | --------- |
| size | int, alt.\* | `400` |
| tooltip_attrs | list | |
| fill | str, alt.\* | `#000` |
| opacity | float, alt.\* | `1` |
| stroke | str, alt.\* | `#565656` |
| strokeWidth | int, alt.\* | `0` |
| halo_offset | int | |
| halo_opacity | float, alt.\* | `1` |
| halo_stroke | str, alt.\* | `#343434` |
| halo_strokeWidth | int, alt.\* | `2` |
| label_attr | str | |
| label_offset | int | `6` |
| label_size | int | `10` |
| label_color | str | `black` |
### Edge args
| arg | type(s) | default |
| ----------- | -------------- | ---------------------------------------------------------------------------------- |
| weight_attr | str | `weight` |
| color | str, alt.\* | `#606060` |
| opacity | float , alt.\* | `alt.Size(weight_attr, scale=alt.Scale(range=[0.3, 1])` if weighted, `1` otherwise |
| strokeWidth | int, alt.\* | `alt.Size(weight_attr, scale=alt.Scale(range=[0.1, 5])` if weighted, `2` otherwise |
---
## Tips
- Get to know your layout algos - especially the 2-3 most used ones. They can have a dramatic
effect on the results. A combination of FA2, Spring and Fruchterman is extremely versatile
if set up right.
- Pass `seed` to layout functions where possible, for repeatable layouts
- Set padding to ensure node elements stay within figure boundaries
## Known limitations
- Node `size` attribute does not support all Altair options - currently only
`alt.value` and `alt.Size` with linear `domain` and `range` scales. More can be
added as needed.
This is a design choice, made to not burden the user with calculating things like
label and halo positions when node sizes vary. Will review this tradeoff based
on in-use experience.
- One combo level currently supported
## See also
- [nx-altair](https://github.com/Zsailer/nx_altair) is a nice project that takes a slightly
different approach to combining NetworkX and Altair for network viz.
نیازمندی
| مقدار | نام |
|---|---|
| >=4.1.0 | altair |
| <4.17 | jsonschema |
| >=2.6.3 | networkx |
| <1.5.0 | pandas |
| >=0.27.1 | scikit-network |
| >=1.10 | pygraphviz |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl alph-0.4.1:
pip install alph-0.4.1.whl
نصب پکیج tar.gz alph-0.4.1:
pip install alph-0.4.1.tar.gz