diff --git a/docs/api/facet-api.ipynb b/docs/api/facet-api.ipynb index 14133e9d..25997c06 100644 --- a/docs/api/facet-api.ipynb +++ b/docs/api/facet-api.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "invalid-london", + "id": "0", "metadata": {}, "source": [ "# Panels and Faceting\n", @@ -13,7 +13,7 @@ { "cell_type": "code", "execution_count": null, - "id": "senior-aruba", + "id": "1", "metadata": { "tags": [] }, @@ -27,7 +27,7 @@ { "cell_type": "code", "execution_count": null, - "id": "alone-purpose", + "id": "2", "metadata": { "tags": [] }, @@ -44,7 +44,7 @@ }, { "cell_type": "markdown", - "id": "removable-shame", + "id": "3", "metadata": {}, "source": [ "## Example graph\n", @@ -55,7 +55,7 @@ { "cell_type": "code", "execution_count": null, - "id": "french-scope", + "id": "4", "metadata": { "tags": [] }, @@ -76,7 +76,7 @@ }, { "cell_type": "markdown", - "id": "foster-skiing", + "id": "5", "metadata": {}, "source": [ "## Non-panel'd version\n", @@ -87,7 +87,7 @@ { "cell_type": "code", "execution_count": null, - "id": "informed-storage", + "id": "6", "metadata": { "tags": [] }, @@ -104,7 +104,7 @@ }, { "cell_type": "markdown", - "id": "hairy-adapter", + "id": "7", "metadata": {}, "source": [ "This isn't particularly useful.\n", @@ -117,7 +117,7 @@ }, { "cell_type": "markdown", - "id": "universal-draft", + "id": "8", "metadata": {}, "source": [ "## `nxviz` faceting API\n", @@ -138,7 +138,7 @@ { "cell_type": "code", "execution_count": null, - "id": "continuing-rochester", + "id": "9", "metadata": { "tags": [] }, @@ -152,7 +152,7 @@ }, { "cell_type": "markdown", - "id": "mounted-daughter", + "id": "10", "metadata": {}, "source": [ "### Arc Panel" @@ -161,7 +161,7 @@ { "cell_type": "code", "execution_count": null, - "id": "improving-alert", + "id": "11", "metadata": { "tags": [] }, @@ -178,7 +178,7 @@ }, { "cell_type": "markdown", - "id": "christian-simon", + "id": "12", "metadata": {}, "source": [ "### Circos Panel" @@ -187,7 +187,7 @@ { "cell_type": "code", "execution_count": null, - "id": "neutral-concentrate", + "id": "13", "metadata": { "tags": [] }, @@ -204,7 +204,7 @@ }, { "cell_type": "markdown", - "id": "silver-buyer", + "id": "14", "metadata": {}, "source": [ "### Matrix Panel" @@ -213,7 +213,7 @@ { "cell_type": "code", "execution_count": null, - "id": "plastic-worcester", + "id": "15", "metadata": {}, "outputs": [], "source": [ @@ -228,7 +228,7 @@ }, { "cell_type": "markdown", - "id": "closing-linux", + "id": "16", "metadata": {}, "source": [ "### Hive Panel\n", @@ -246,7 +246,7 @@ { "cell_type": "code", "execution_count": null, - "id": "common-rocket", + "id": "17", "metadata": { "tags": [] }, @@ -257,7 +257,7 @@ }, { "cell_type": "markdown", - "id": "compliant-smart", + "id": "18", "metadata": {}, "source": [ "## Custom panels\n", @@ -276,7 +276,7 @@ { "cell_type": "code", "execution_count": null, - "id": "motivated-cassette", + "id": "19", "metadata": { "tags": [] }, @@ -292,7 +292,7 @@ { "cell_type": "code", "execution_count": null, - "id": "assumed-government", + "id": "20", "metadata": { "tags": [] }, @@ -323,7 +323,7 @@ }, { "cell_type": "markdown", - "id": "beneficial-antarctica", + "id": "21", "metadata": {}, "source": [ "## Development pattern\n", @@ -341,7 +341,7 @@ { "cell_type": "code", "execution_count": null, - "id": "bigger-middle", + "id": "22", "metadata": { "tags": [] }, @@ -354,7 +354,7 @@ }, { "cell_type": "markdown", - "id": "naval-retro", + "id": "23", "metadata": {}, "source": [ "The pattern is essentially to identify the exact groups that exist,\n", diff --git a/docs/api/high-level-api.ipynb b/docs/api/high-level-api.ipynb index cf7761a1..d2e96603 100644 --- a/docs/api/high-level-api.ipynb +++ b/docs/api/high-level-api.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "painted-david", + "id": "0", "metadata": {}, "source": [ "# High Level API\n", @@ -25,7 +25,7 @@ }, { "cell_type": "markdown", - "id": "junior-sociology", + "id": "1", "metadata": {}, "source": [ "## How to read this notebook\n", @@ -40,7 +40,7 @@ { "cell_type": "code", "execution_count": null, - "id": "cross-photographer", + "id": "2", "metadata": { "tags": [] }, @@ -54,7 +54,7 @@ { "cell_type": "code", "execution_count": null, - "id": "collectible-chambers", + "id": "3", "metadata": { "tags": [] }, @@ -73,7 +73,7 @@ }, { "cell_type": "markdown", - "id": "greenhouse-flexibility", + "id": "4", "metadata": {}, "source": [ "## Example Graph\n", @@ -84,7 +84,7 @@ }, { "cell_type": "markdown", - "id": "scientific-rates", + "id": "5", "metadata": {}, "source": [ "### Source code\n", @@ -95,7 +95,7 @@ { "cell_type": "code", "execution_count": null, - "id": "israeli-helping", + "id": "6", "metadata": { "tags": [] }, @@ -117,7 +117,7 @@ }, { "cell_type": "markdown", - "id": "linear-religion", + "id": "7", "metadata": {}, "source": [ "### Node table" @@ -126,7 +126,7 @@ { "cell_type": "code", "execution_count": null, - "id": "manufactured-steel", + "id": "8", "metadata": { "tags": [] }, @@ -140,7 +140,7 @@ { "cell_type": "code", "execution_count": null, - "id": "recorded-virginia", + "id": "9", "metadata": { "tags": [] }, @@ -151,7 +151,7 @@ }, { "cell_type": "markdown", - "id": "twelve-retro", + "id": "10", "metadata": {}, "source": [ "## Hive Plot\n", @@ -171,7 +171,7 @@ { "cell_type": "code", "execution_count": null, - "id": "textile-settlement", + "id": "11", "metadata": { "tags": [] }, @@ -189,7 +189,7 @@ }, { "cell_type": "markdown", - "id": "distinguished-behavior", + "id": "12", "metadata": {}, "source": [ "Here's an alternative visualization where\n", @@ -201,7 +201,7 @@ { "cell_type": "code", "execution_count": null, - "id": "sophisticated-shelter", + "id": "13", "metadata": { "tags": [] }, @@ -216,7 +216,7 @@ }, { "cell_type": "markdown", - "id": "occasional-newsletter", + "id": "14", "metadata": {}, "source": [ "The same consistent API applies to the other plot types." @@ -224,7 +224,7 @@ }, { "cell_type": "markdown", - "id": "tropical-lawyer", + "id": "15", "metadata": {}, "source": [ "## Arc Plot" @@ -233,7 +233,7 @@ { "cell_type": "code", "execution_count": null, - "id": "individual-chapel", + "id": "16", "metadata": { "tags": [] }, @@ -250,7 +250,7 @@ }, { "cell_type": "markdown", - "id": "about-raising", + "id": "17", "metadata": {}, "source": [ "## Circos Plot" @@ -259,7 +259,7 @@ { "cell_type": "code", "execution_count": null, - "id": "three-volleyball", + "id": "18", "metadata": { "tags": [] }, @@ -277,7 +277,7 @@ }, { "cell_type": "markdown", - "id": "understood-adjustment", + "id": "19", "metadata": {}, "source": [ "## Matrix Plot" @@ -286,7 +286,7 @@ { "cell_type": "code", "execution_count": null, - "id": "previous-shopping", + "id": "20", "metadata": { "tags": [] }, @@ -313,7 +313,7 @@ { "cell_type": "code", "execution_count": null, - "id": "renewable-quilt", + "id": "21", "metadata": {}, "outputs": [], "source": [] diff --git a/docs/api/low-level-api.ipynb b/docs/api/low-level-api.ipynb index e3dd0d2d..aa9bd5ad 100644 --- a/docs/api/low-level-api.ipynb +++ b/docs/api/low-level-api.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "molecular-letters", + "id": "0", "metadata": {}, "source": [ "# Low-level API\n", @@ -21,7 +21,7 @@ { "cell_type": "code", "execution_count": null, - "id": "beginning-supplement", + "id": "1", "metadata": {}, "outputs": [], "source": [ @@ -32,7 +32,7 @@ }, { "cell_type": "markdown", - "id": "joined-james", + "id": "2", "metadata": {}, "source": [ "## Example\n", @@ -47,7 +47,7 @@ { "cell_type": "code", "execution_count": null, - "id": "blank-criterion", + "id": "3", "metadata": { "tags": [] }, @@ -70,7 +70,7 @@ }, { "cell_type": "markdown", - "id": "restricted-terminology", + "id": "4", "metadata": {}, "source": [ "## Node and Edge Table\n", @@ -82,7 +82,7 @@ { "cell_type": "code", "execution_count": null, - "id": "operating-movie", + "id": "5", "metadata": {}, "outputs": [], "source": [ @@ -94,7 +94,7 @@ }, { "cell_type": "markdown", - "id": "organic-anniversary", + "id": "6", "metadata": {}, "source": [ "The node table is indexed by node ID, and all of the metadata attributes are stored as columns." @@ -103,7 +103,7 @@ { "cell_type": "code", "execution_count": null, - "id": "applicable-retention", + "id": "7", "metadata": {}, "outputs": [], "source": [ @@ -113,7 +113,7 @@ }, { "cell_type": "markdown", - "id": "historical-aerospace", + "id": "8", "metadata": {}, "source": [ "For the edge table, the \"source\" and \"target\" columns are the node IDs in the node table.\n", @@ -123,7 +123,7 @@ }, { "cell_type": "markdown", - "id": "rotary-stage", + "id": "9", "metadata": {}, "source": [ "## Circos layout\n", @@ -143,7 +143,7 @@ { "cell_type": "code", "execution_count": null, - "id": "curious-rebound", + "id": "10", "metadata": { "tags": [] }, @@ -156,7 +156,7 @@ }, { "cell_type": "markdown", - "id": "colored-daisy", + "id": "11", "metadata": {}, "source": [ "## Node styling\n", @@ -193,7 +193,7 @@ { "cell_type": "code", "execution_count": null, - "id": "objective-melissa", + "id": "12", "metadata": { "tags": [] }, @@ -223,7 +223,7 @@ }, { "cell_type": "markdown", - "id": "premium-volunteer", + "id": "13", "metadata": {}, "source": [ "We can now combine everything together, into something that basically reconstructs\n", @@ -233,7 +233,7 @@ { "cell_type": "code", "execution_count": null, - "id": "modern-visitor", + "id": "14", "metadata": { "tags": [] }, @@ -249,7 +249,7 @@ { "cell_type": "code", "execution_count": null, - "id": "thirty-phone", + "id": "15", "metadata": { "tags": [] }, @@ -274,7 +274,7 @@ }, { "cell_type": "markdown", - "id": "latin-delta", + "id": "16", "metadata": {}, "source": [ "Voila! We now have a sonic hedgehog-style node layout! Pretty cool, isn't it?" @@ -282,7 +282,7 @@ }, { "cell_type": "markdown", - "id": "liked-sentence", + "id": "17", "metadata": {}, "source": [ "## Adding in edges" @@ -290,7 +290,7 @@ }, { "cell_type": "markdown", - "id": "imperial-satin", + "id": "18", "metadata": {}, "source": [ "Once the node layout is complete, customizing the edge styling is a matter of concerning ourselves with:\n", @@ -307,7 +307,7 @@ { "cell_type": "code", "execution_count": null, - "id": "annoying-center", + "id": "19", "metadata": { "tags": [] }, @@ -321,7 +321,7 @@ { "cell_type": "code", "execution_count": null, - "id": "persistent-farming", + "id": "20", "metadata": { "tags": [] }, @@ -361,7 +361,7 @@ }, { "cell_type": "markdown", - "id": "alpha-yesterday", + "id": "21", "metadata": {}, "source": [ "Looking at the plot, we might find that expressing the edges' `edge_value` as line width might not be that effective. Instead, we might want to express it using alpha." @@ -370,7 +370,7 @@ { "cell_type": "code", "execution_count": null, - "id": "laden-electricity", + "id": "22", "metadata": { "tags": [] }, @@ -410,7 +410,7 @@ }, { "cell_type": "markdown", - "id": "interracial-documentation", + "id": "23", "metadata": {}, "source": [ "Looking at this plot, it's a lot easier for us to see the important edges (as visualized by the alpha value)." @@ -418,7 +418,7 @@ }, { "cell_type": "markdown", - "id": "agreed-receipt", + "id": "24", "metadata": {}, "source": [ "## Conclusion\n", diff --git a/docs/api/mid-level-api.ipynb b/docs/api/mid-level-api.ipynb index 140355f1..218872a4 100644 --- a/docs/api/mid-level-api.ipynb +++ b/docs/api/mid-level-api.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "fiscal-winning", + "id": "0", "metadata": {}, "source": [ "# Mid-Level API\n", @@ -33,7 +33,7 @@ { "cell_type": "code", "execution_count": null, - "id": "narrow-football", + "id": "1", "metadata": { "tags": [] }, @@ -46,7 +46,7 @@ }, { "cell_type": "markdown", - "id": "essential-reason", + "id": "2", "metadata": {}, "source": [ "## An example graph\n", @@ -57,7 +57,7 @@ { "cell_type": "code", "execution_count": null, - "id": "compliant-platinum", + "id": "3", "metadata": { "tags": [] }, @@ -71,7 +71,7 @@ { "cell_type": "code", "execution_count": null, - "id": "golden-jacket", + "id": "4", "metadata": { "tags": [] }, @@ -120,7 +120,7 @@ }, { "cell_type": "markdown", - "id": "proprietary-naples", + "id": "5", "metadata": {}, "source": [ "### Visualization using NetworkX's built-in facilities\n", @@ -132,7 +132,7 @@ { "cell_type": "code", "execution_count": null, - "id": "productive-history", + "id": "6", "metadata": { "tags": [] }, @@ -143,7 +143,7 @@ }, { "cell_type": "markdown", - "id": "ready-exclusive", + "id": "7", "metadata": {}, "source": [ "That looks a bit like a hairball. How can we make it look nicer?" @@ -151,7 +151,7 @@ }, { "cell_type": "markdown", - "id": "clean-newspaper", + "id": "8", "metadata": {}, "source": [ "## Node Layout\n", @@ -175,7 +175,7 @@ { "cell_type": "code", "execution_count": null, - "id": "ancient-mississippi", + "id": "9", "metadata": { "tags": [] }, @@ -188,7 +188,7 @@ }, { "cell_type": "markdown", - "id": "cathedral-humor", + "id": "10", "metadata": {}, "source": [ "Right now, it doesn't look like much - a blue donut, basically.\n", @@ -208,7 +208,7 @@ { "cell_type": "code", "execution_count": null, - "id": "usual-suffering", + "id": "11", "metadata": { "tags": [] }, @@ -219,7 +219,7 @@ }, { "cell_type": "markdown", - "id": "champion-oracle", + "id": "12", "metadata": {}, "source": [ "You might be wondering, why didn't that do anything?\n", @@ -238,7 +238,7 @@ { "cell_type": "code", "execution_count": null, - "id": "limiting-stanley", + "id": "13", "metadata": { "tags": [] }, @@ -249,7 +249,7 @@ }, { "cell_type": "markdown", - "id": "infrared-poverty", + "id": "14", "metadata": {}, "source": [ "Things are starting to look promising!\n", @@ -262,7 +262,7 @@ { "cell_type": "code", "execution_count": null, - "id": "vanilla-programmer", + "id": "15", "metadata": { "tags": [] }, @@ -273,7 +273,7 @@ }, { "cell_type": "markdown", - "id": "dense-spending", + "id": "16", "metadata": {}, "source": [ "The nodes look a bit more appropriately sized!\n", @@ -288,7 +288,7 @@ { "cell_type": "code", "execution_count": null, - "id": "latin-vampire", + "id": "17", "metadata": { "tags": [] }, @@ -302,7 +302,7 @@ }, { "cell_type": "markdown", - "id": "adequate-programming", + "id": "18", "metadata": {}, "source": [ "Putting it together with `aspect_equal()` will get us to a good starting point." @@ -311,7 +311,7 @@ { "cell_type": "code", "execution_count": null, - "id": "future-composer", + "id": "19", "metadata": { "tags": [] }, @@ -324,7 +324,7 @@ }, { "cell_type": "markdown", - "id": "handled-manchester", + "id": "20", "metadata": {}, "source": [ "_Voila!_\n", @@ -350,7 +350,7 @@ { "cell_type": "code", "execution_count": null, - "id": "arbitrary-convention", + "id": "21", "metadata": { "tags": [] }, @@ -367,7 +367,7 @@ }, { "cell_type": "markdown", - "id": "superior-carnival", + "id": "22", "metadata": {}, "source": [ "An alternative to drawing circos edges is to draw lines directly for each edge." @@ -376,7 +376,7 @@ { "cell_type": "code", "execution_count": null, - "id": "governmental-chorus", + "id": "23", "metadata": { "tags": [] }, @@ -391,7 +391,7 @@ }, { "cell_type": "markdown", - "id": "later-guess", + "id": "24", "metadata": {}, "source": [ "Regardless of which edge drawing method we choose,\n", @@ -404,7 +404,7 @@ { "cell_type": "code", "execution_count": null, - "id": "exclusive-filename", + "id": "25", "metadata": { "tags": [] }, @@ -422,7 +422,7 @@ }, { "cell_type": "markdown", - "id": "superb-grenada", + "id": "26", "metadata": {}, "source": [ "Now it is clear that there are quite a lot of within-conference edges,\n", @@ -431,7 +431,7 @@ }, { "cell_type": "markdown", - "id": "special-sewing", + "id": "27", "metadata": {}, "source": [ "## Other layouts" @@ -439,7 +439,7 @@ }, { "cell_type": "markdown", - "id": "seeing-emergency", + "id": "28", "metadata": {}, "source": [ "### Arc layout" @@ -448,7 +448,7 @@ { "cell_type": "code", "execution_count": null, - "id": "fleet-wellington", + "id": "29", "metadata": { "tags": [] }, @@ -464,7 +464,7 @@ }, { "cell_type": "markdown", - "id": "typical-malawi", + "id": "30", "metadata": {}, "source": [ "### Parallel coordinates layout" @@ -473,7 +473,7 @@ { "cell_type": "code", "execution_count": null, - "id": "disturbed-swedish", + "id": "31", "metadata": { "tags": [] }, @@ -490,7 +490,7 @@ }, { "cell_type": "markdown", - "id": "according-provision", + "id": "32", "metadata": {}, "source": [ "The parallel coordinates layout might not necessarily be the most informative for this graph dataset,\n", @@ -501,7 +501,7 @@ }, { "cell_type": "markdown", - "id": "cognitive-christian", + "id": "33", "metadata": {}, "source": [ "## Hive plot layout\n", @@ -521,7 +521,7 @@ { "cell_type": "code", "execution_count": null, - "id": "recovered-michael", + "id": "34", "metadata": { "tags": [] }, @@ -555,7 +555,7 @@ }, { "cell_type": "markdown", - "id": "anticipated-tyler", + "id": "35", "metadata": {}, "source": [ "And here, we see an interesting pattern show up that might not have been visible earlier on:\n", @@ -565,7 +565,7 @@ }, { "cell_type": "markdown", - "id": "sized-professional", + "id": "36", "metadata": {}, "source": [ "## Conclusions\n", diff --git a/docs/api/object-oriented-api.ipynb b/docs/api/object-oriented-api.ipynb index 832135e6..1fb2b8f8 100644 --- a/docs/api/object-oriented-api.ipynb +++ b/docs/api/object-oriented-api.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "aware-watershed", + "id": "0", "metadata": {}, "source": [ "# Object-Oriented API\n", @@ -13,7 +13,7 @@ { "cell_type": "code", "execution_count": null, - "id": "synthetic-karaoke", + "id": "1", "metadata": { "tags": [] }, @@ -27,7 +27,7 @@ { "cell_type": "code", "execution_count": null, - "id": "practical-female", + "id": "2", "metadata": { "tags": [] }, @@ -46,7 +46,7 @@ }, { "cell_type": "markdown", - "id": "written-jerusalem", + "id": "3", "metadata": {}, "source": [ "## Example Graph\n", @@ -57,7 +57,7 @@ }, { "cell_type": "markdown", - "id": "adjacent-glory", + "id": "4", "metadata": {}, "source": [ "### Source code\n" @@ -66,7 +66,7 @@ { "cell_type": "code", "execution_count": null, - "id": "divine-humanity", + "id": "5", "metadata": { "tags": [] }, @@ -84,7 +84,7 @@ }, { "cell_type": "markdown", - "id": "finite-trustee", + "id": "6", "metadata": {}, "source": [ "## API Examples\n", @@ -105,7 +105,7 @@ { "cell_type": "code", "execution_count": null, - "id": "protecting-treasury", + "id": "7", "metadata": { "tags": [] }, @@ -120,7 +120,7 @@ { "cell_type": "code", "execution_count": null, - "id": "alert-capture", + "id": "8", "metadata": { "tags": [] }, @@ -132,7 +132,7 @@ { "cell_type": "code", "execution_count": null, - "id": "grand-orlando", + "id": "9", "metadata": { "tags": [] }, @@ -144,7 +144,7 @@ { "cell_type": "code", "execution_count": null, - "id": "wicked-photographer", + "id": "10", "metadata": { "tags": [] }, diff --git a/docs/developers/new-plots.ipynb b/docs/developers/new-plots.ipynb index d2f7ff59..88edbf0f 100644 --- a/docs/developers/new-plots.ipynb +++ b/docs/developers/new-plots.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "apart-distribution", + "id": "0", "metadata": {}, "source": [ "# Implementing a new plot\n", @@ -16,7 +16,7 @@ { "cell_type": "code", "execution_count": null, - "id": "worst-abuse", + "id": "1", "metadata": {}, "outputs": [], "source": [ @@ -27,7 +27,7 @@ }, { "cell_type": "markdown", - "id": "clinical-agenda", + "id": "2", "metadata": {}, "source": [ "## Example graph\n", @@ -38,7 +38,7 @@ { "cell_type": "code", "execution_count": null, - "id": "nervous-quest", + "id": "3", "metadata": { "tags": [] }, @@ -61,7 +61,7 @@ }, { "cell_type": "markdown", - "id": "neither-bolivia", + "id": "4", "metadata": {}, "source": [ "## Implement node layout\n", @@ -93,7 +93,7 @@ { "cell_type": "code", "execution_count": null, - "id": "elegant-nudist", + "id": "5", "metadata": { "tags": [] }, @@ -115,7 +115,7 @@ }, { "cell_type": "markdown", - "id": "imperial-mounting", + "id": "6", "metadata": {}, "source": [ "With a matrix plot, our goal is to place nodes along the x- and y-axis.\n", @@ -127,7 +127,7 @@ { "cell_type": "code", "execution_count": null, - "id": "mineral-worthy", + "id": "7", "metadata": { "tags": [] }, @@ -159,7 +159,7 @@ }, { "cell_type": "markdown", - "id": "related-healing", + "id": "8", "metadata": {}, "source": [ "Now that we have the positions implemented, let's see what they look like." @@ -168,7 +168,7 @@ { "cell_type": "code", "execution_count": null, - "id": "noted-strain", + "id": "9", "metadata": { "tags": [] }, @@ -185,7 +185,7 @@ { "cell_type": "code", "execution_count": null, - "id": "direct-class", + "id": "10", "metadata": { "tags": [] }, @@ -197,7 +197,7 @@ { "cell_type": "code", "execution_count": null, - "id": "imported-harmony", + "id": "11", "metadata": { "tags": [] }, @@ -208,7 +208,7 @@ }, { "cell_type": "markdown", - "id": "satisfied-walnut", + "id": "12", "metadata": {}, "source": [ "Now, we can worry about the glyphs being drawn to screen.\n", @@ -220,7 +220,7 @@ { "cell_type": "code", "execution_count": null, - "id": "departmental-platform", + "id": "13", "metadata": { "tags": [] }, @@ -234,7 +234,7 @@ { "cell_type": "code", "execution_count": null, - "id": "utility-collect", + "id": "14", "metadata": { "tags": [] }, @@ -249,7 +249,7 @@ }, { "cell_type": "markdown", - "id": "collective-advisory", + "id": "15", "metadata": {}, "source": [ "Not bad! We're off to a good start.\n", @@ -260,7 +260,7 @@ { "cell_type": "code", "execution_count": null, - "id": "disabled-lyric", + "id": "16", "metadata": { "tags": [] }, @@ -280,7 +280,7 @@ }, { "cell_type": "markdown", - "id": "running-orleans", + "id": "17", "metadata": {}, "source": [ "Now that's looking good! We have a square matrix, just as we expected." @@ -288,7 +288,7 @@ }, { "cell_type": "markdown", - "id": "stone-refund", + "id": "18", "metadata": {}, "source": [ "## Drawing edges\n", @@ -301,7 +301,7 @@ { "cell_type": "code", "execution_count": null, - "id": "colored-assist", + "id": "19", "metadata": { "tags": [] }, @@ -319,7 +319,7 @@ }, { "cell_type": "markdown", - "id": "dense-johnson", + "id": "20", "metadata": {}, "source": [ "However, the spirit of a matrix plot is to fill in an `n-by-n` matrix.\n", @@ -333,7 +333,7 @@ { "cell_type": "code", "execution_count": null, - "id": "cosmetic-victory", + "id": "21", "metadata": { "tags": [] }, @@ -394,7 +394,7 @@ }, { "cell_type": "markdown", - "id": "detailed-mistress", + "id": "22", "metadata": {}, "source": [ "## Annotations\n", @@ -406,7 +406,7 @@ }, { "cell_type": "markdown", - "id": "polar-honor", + "id": "23", "metadata": {}, "source": [ "### Node color by group" @@ -415,7 +415,7 @@ { "cell_type": "code", "execution_count": null, - "id": "pacific-teacher", + "id": "24", "metadata": { "tags": [] }, @@ -443,7 +443,7 @@ }, { "cell_type": "markdown", - "id": "residential-convention", + "id": "25", "metadata": {}, "source": [ "### Node color by value" @@ -452,7 +452,7 @@ { "cell_type": "code", "execution_count": null, - "id": "removed-chocolate", + "id": "26", "metadata": { "tags": [] }, @@ -480,7 +480,7 @@ }, { "cell_type": "markdown", - "id": "unlike-underwear", + "id": "27", "metadata": {}, "source": [ "### Annotating group identity\n", @@ -492,7 +492,7 @@ { "cell_type": "code", "execution_count": null, - "id": "tender-retro", + "id": "28", "metadata": { "tags": [] }, @@ -544,7 +544,7 @@ }, { "cell_type": "markdown", - "id": "color-swiss", + "id": "29", "metadata": {}, "source": [ "### Annotate matrix blocks\n", @@ -558,7 +558,7 @@ { "cell_type": "code", "execution_count": null, - "id": "composed-lafayette", + "id": "30", "metadata": { "tags": [] }, @@ -627,7 +627,7 @@ }, { "cell_type": "markdown", - "id": "metallic-storage", + "id": "31", "metadata": {}, "source": [ "## High level API\n", @@ -640,7 +640,7 @@ { "cell_type": "code", "execution_count": null, - "id": "cellular-concept", + "id": "32", "metadata": { "tags": [] }, @@ -654,7 +654,7 @@ { "cell_type": "code", "execution_count": null, - "id": "looking-formation", + "id": "33", "metadata": { "tags": [] }, diff --git a/docs/examples/geo.ipynb b/docs/examples/geo.ipynb index 19d6346f..a2100cca 100644 --- a/docs/examples/geo.ipynb +++ b/docs/examples/geo.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "prepared-symbol", + "id": "0", "metadata": {}, "source": [ "## Geo Plot\n", @@ -14,7 +14,7 @@ { "cell_type": "code", "execution_count": null, - "id": "permanent-shift", + "id": "1", "metadata": { "tags": [] }, @@ -28,7 +28,7 @@ { "cell_type": "code", "execution_count": null, - "id": "broad-robinson", + "id": "2", "metadata": { "tags": [] }, @@ -45,7 +45,7 @@ { "cell_type": "code", "execution_count": null, - "id": "laughing-lindsay", + "id": "3", "metadata": { "tags": [] }, @@ -61,7 +61,7 @@ }, { "cell_type": "markdown", - "id": "numerical-cross", + "id": "4", "metadata": {}, "source": [ "## Mid-level API" @@ -70,7 +70,7 @@ { "cell_type": "code", "execution_count": null, - "id": "dental-walker", + "id": "5", "metadata": { "tags": [] }, @@ -94,7 +94,7 @@ }, { "cell_type": "markdown", - "id": "stuck-evolution", + "id": "6", "metadata": {}, "source": [ "## High-level API" @@ -103,7 +103,7 @@ { "cell_type": "code", "execution_count": null, - "id": "worst-tragedy", + "id": "7", "metadata": { "tags": [] }, diff --git a/docs/examples/matrix.ipynb b/docs/examples/matrix.ipynb index ec4148c9..0b0cbc3a 100644 --- a/docs/examples/matrix.ipynb +++ b/docs/examples/matrix.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "regional-perfume", + "id": "0", "metadata": {}, "source": [ "# Matrix Plot\n", @@ -13,7 +13,7 @@ { "cell_type": "code", "execution_count": null, - "id": "protecting-subdivision", + "id": "1", "metadata": { "tags": [] }, @@ -27,7 +27,7 @@ { "cell_type": "code", "execution_count": null, - "id": "rational-liability", + "id": "2", "metadata": { "tags": [] }, @@ -43,7 +43,7 @@ { "cell_type": "code", "execution_count": null, - "id": "corresponding-belarus", + "id": "3", "metadata": { "tags": [] }, @@ -58,7 +58,7 @@ { "cell_type": "code", "execution_count": null, - "id": "absolute-universe", + "id": "4", "metadata": { "tags": [] }, diff --git a/examples/circos/edge_color.py b/examples/circos/edge_color.py index aad02648..6abb2db2 100644 --- a/examples/circos/edge_color.py +++ b/examples/circos/edge_color.py @@ -1,6 +1,7 @@ """ Shows different edge colors. Either categorial/ordinal or continuous """ + import matplotlib.pyplot as plt import networkx as nx from nxviz.plots import CircosPlot diff --git a/examples/circos/edge_width.py b/examples/circos/edge_width.py index 64b7228a..ed265509 100644 --- a/examples/circos/edge_width.py +++ b/examples/circos/edge_width.py @@ -1,6 +1,7 @@ """ Shows different edge widths on CircusPlot """ + import matplotlib.pyplot as plt import networkx as nx from nxviz.plots import CircosPlot diff --git a/nxviz/__init__.py b/nxviz/__init__.py index 979f8f92..69b1f632 100644 --- a/nxviz/__init__.py +++ b/nxviz/__init__.py @@ -1,4 +1,5 @@ """Top-level nxviz API.""" + from .api import ( arc, hive, diff --git a/nxviz/annotate.py b/nxviz/annotate.py index 9373460f..57c149c3 100644 --- a/nxviz/annotate.py +++ b/nxviz/annotate.py @@ -1,4 +1,5 @@ """Annotation submodule.""" + from functools import partial, update_wrapper from typing import Dict, Hashable diff --git a/nxviz/api.py b/nxviz/api.py index 08486044..acaa4c59 100644 --- a/nxviz/api.py +++ b/nxviz/api.py @@ -1,6 +1,5 @@ """High level nxviz plotting API.""" - from functools import partial, update_wrapper from typing import Callable, Dict, Hashable diff --git a/nxviz/encodings.py b/nxviz/encodings.py index b73987d5..9386c08e 100644 --- a/nxviz/encodings.py +++ b/nxviz/encodings.py @@ -1,4 +1,5 @@ """Functions to encode data inside visual properties of nodes and edges.""" + from functools import partial from typing import Callable, Tuple diff --git a/nxviz/facet.py b/nxviz/facet.py index 7f835ae8..387f3263 100644 --- a/nxviz/facet.py +++ b/nxviz/facet.py @@ -6,6 +6,7 @@ The others are faceting functions that can be called on. The faceting functions rely on the high level API for plotting. """ + import warnings from functools import partial, update_wrapper from itertools import combinations diff --git a/nxviz/geometry.py b/nxviz/geometry.py index e1960de8..d6f79d66 100644 --- a/nxviz/geometry.py +++ b/nxviz/geometry.py @@ -1,6 +1,7 @@ """ Utility geometry functions that can help with drawing to screen. """ + import numpy as np from .polcart import to_cartesian diff --git a/nxviz/io.py b/nxviz/io.py index 1d6b2cba..2e1c9dcf 100644 --- a/nxviz/io.py +++ b/nxviz/io.py @@ -1,4 +1,5 @@ """Deprecated module no longer used.""" + import pandas as pd from networkx import Graph, MultiGraph diff --git a/nxviz/lines.py b/nxviz/lines.py index d7fba70e..a601b43a 100644 --- a/nxviz/lines.py +++ b/nxviz/lines.py @@ -1,6 +1,5 @@ """Patch generators for edges.""" - from itertools import product from typing import Dict, Iterable, List diff --git a/nxviz/utils.py b/nxviz/utils.py index 1e31564d..47660837 100644 --- a/nxviz/utils.py +++ b/nxviz/utils.py @@ -1,4 +1,5 @@ """Utility functions.""" + from collections import Counter import pandas as pd diff --git a/tests/conftest.py b/tests/conftest.py index 7f14ea05..9cc9ec9b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,2 +1,3 @@ """Pytest configuration.""" + from .fixtures.graphs import dummyG, geoG, manygroupG, smallG diff --git a/tests/test_midlevel_api.py b/tests/test_midlevel_api.py index e6492c83..f5f96998 100644 --- a/tests/test_midlevel_api.py +++ b/tests/test_midlevel_api.py @@ -1,6 +1,5 @@ """Integration tests that operate at the mid-level API.""" - from nxviz import nodes, edges import pytest diff --git a/tests/test_polcart.py b/tests/test_polcart.py index 4f05a6a6..f7a7d81c 100644 --- a/tests/test_polcart.py +++ b/tests/test_polcart.py @@ -1,4 +1,5 @@ """Tests for polcart submodule.""" + import numpy as np from hypothesis import assume, given, settings