Graphviz Python

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  1. Graphviz Python Install
  2. Using Graphviz In Python
  3. Graphviz Python Show
  4. Graphviz Python Save Image

A vscode extension that provides language support and live preview for the Graphviz format.

Download graphviz-python packages for CentOS, openSUSE. OpenSUSE Oss x8664 Official graphviz-python-2.40.1-6.6.8.aarch64.rpm: Python Extension for Graphviz. Graphvizdotargs ¶ Additional command-line arguments to give to dot, as a list. The default is an empty list. This is the right place to set global graph, node or edge attributes via dot’s -G, -N and -E options. Graphvizoutputformat ¶ The output format for Graphviz when building HTML files. This must be either 'png' or 'svg'; the default. Conda install -c anaconda python-graphviz Description. This package facilitates the creation and rendering of graph descriptions in the DOT language of the Graphviz graph drawing software from Python. By data scientists, for data scientists. About Us Anaconda Nucleus Download Anaconda. Conda install linux-64 v0.8.4; win-32 v0.8.2; noarch v0.16; win-64 v0.8.4; osx-64 v0.8.4; To install this package with conda run one of the following: conda install -c conda-forge python-graphviz.

The preview uses the Viz.js library.

The extension can be activated in two ways

Features

Snippets

Try typing one of the following prefixes to see available snippets: graph, >, var, dir, prop, path or rank and efficiently create graphs, variables, properties, paths or ranks.

Graph preview

Graphviz Python Install

  • Toggle Preview - ctrl+shift+v (Mac: cmd+shift+v)
  • Open Preview to the Side - ctrl+k v (Mac: cmd+k shift+v)

ctrl+f is supported to search for nodes/edges in large graphs, but it is best first to reset the scale to [1:1].

Scaling the graph preview

The live preview of the graph can now be:

  • scaled up [▲],
  • scaled down [▼],
  • reset to 1:1 (one-to-one) scale,
  • scaled to fit the width of the pane [↔] or
  • scaled to fit the height of the pane [↕].

This greatly facilitates viewing large graphs.

To facilitate working on graph files in the editor, or visualizing files that are created by programs (i.e. search algorithms), the preview can be auto-scaled:

Double clicking on the fit-to-width [↔] or fit-to-height [↕] buttons toggles the given mode on, so when the graph source changes, the preview scales automatically to remain visible.

The zoom level value may be now set to a specific value, or gradually changed by the up/down keys on the keyboard.

Exporting to a .svg file

Click the [↓] button and select the location of the .svg file. The file may be open in any web browser, or attached to an email etc...

Opening preview in a browser

It is also possible to open the file in the default browser by clicking on [⇱]. This creates a temp file and asks the operating system to open it in a default browser or another capable application.

Known issues:

  • When VS Code window is re-sized, the auto-scaling does not kick-in as there is no VS Code event that we can listen to. Workaround: click the button again (the toggle state does not change).
  • After the zoom percentage is set manually, the zoom value does no longer update when pressing other toolbar buttons. However, the display continues scaling as expected.

For other extension developers

Other extensions may invoke the preview pane programmatically by writing a valid .dot file to the disk and then executing this command:

How to install

Launch VS Code Quick Open (Ctrl+P), paste the following command, and press enter:

ext install joaompinto.vscode-graphviz

How to build and install from source (Linux)

On Windows, just omit the sudo instruction.

Credits

  • The preview uses https://github.com/mdaines/viz.js/ .
  • The syntax highlight/snippets support is based on https://github.com/Stephanvs/vscode-graphviz .
  • HTML-Like Labels
    • HTML-Like Label Examples

There are three main types of shapes :polygon-based,record-based anduser-defined.The record-based shape has largely been superseded and greatly generalizedby HTML-like labels.That is, instead of using shape=record, one mightconsider using shape=none, margin=0 and an HTML-like label.

The geometry and style of all node shapes are affected bythe node attributes fixedsize,fontname,fontsize,height,label,style andwidth.

Polygon-based Nodes

The possible polygon-based shapes are displayed below.

As the figures suggest, the shapes rect and rectangle are synonyms for box, and none is a synonym for plaintext.The shape plain is similar to these two, except that it also enforceswidth=0 height=0 margin=0, which guarantees that the actual size of the node is entirely determined by the label.This is useful, for example, when using HTML-like labels.Also, unlike the rest, we have shown these three, as well as underline,without style=filledto indicate the normal use. If fill were turned on, the label text wouldappear in a filled rectangle.

The geometries of polygon-based shapes are also affectedby the node attributes regular,peripheries andorientation.If shape='polygon', the attributessides,skew anddistortion are also used.If unset, they default to 4, 0.0 and 0.0, respectively.The point shape is special in that it isonly affected by the peripheries,width andheight attributes.

Normally, the size of a node is determined by smallest width and heightneeded to contain its label and image, if any, with a margin specified bythe margin attribute. The widthand height must also be at least as large as the sizes specified by thewidth andheight attributes, which specifythe minimum values for these parameters. See the fixedsize attributefor ways of restricting the node size.In particular, if fixedsize=shape, the node’s shape will be fixedby the width andheight attributes, and the shapeis used for edge termination, but both the shape and label sizes are usedpreventing node overlap. For example, the following graph:

yields the figure:

Note that the label of the yellow node, with fixedsize=true, overlapsthe other node, where there is sufficient space for the gray node withfixedsize=shape.

The shapes: note, tab, folder,box3d and component were provided by Pander.The synthetic biology shapes:promoter,cds,terminator,utr,primersite,restrictionsite,fivepoverhang,threepoverhang,noverhang,assembly,signature,insulator,ribosite,rnastab,proteasesite,proteinstab,rpromoter,rarrow,larrow andlpromoterwere contributed by Jenny Cheng.

Record-based Nodes

NOTE: Please see the note about record-based nodes at thetop of this page. Also note that there are problems usingnon-trivial edges (edges with ports or labels) between adjacentnodes on the same rank if one or both nodes has a record shape.

These are specified by shape values of “record” and “Mrecord”.The structure of a record-based node is determined by its label,which has the following schema:

rlabel=field ( ' ' field )*
where field=fieldId or '{' rlabel '}'
and fieldId= [ '<' string '>'] [ string ]

Braces, vertical bars and angle brackets must be escaped witha backslash character if you wish them to appear as a literal character.Spaces are interpreted as separators between tokens,so they must be escaped if you want spaces in the text.

The first string in fieldId assigns a portname to the field and canbe combined with the node name to indicate where to attach an edgeto the node. (See portPos.)The second string is used as the text for the field; it supports the usualescape sequencesn, l and r.

Visually, a record is a box, with fields represented by alternatingrows of horizontal or vertical subboxes. The Mrecord shape is identicalto a record shape, except that the outermost box has rounded corners.Flipping between horizontal and vertical layouts is done by nestingfields in braces “{…}”. The top-level orientation in a record ishorizontal. Thus, a record with label “A B C D” will have 4 fields oriented left to right, while “{A B C D}” will have them from top to bottom and “A { B C } D” will have “B” over “C”, with“A” to the left and “D” to the right of “B” and “C”.

The initial orientation of a record node depends on therankdir attribute. If this attributeis TB (the default) or BT, corresponding to verticallayouts, the top-level fields in a record are displayed horizontally.If, however, this attribute is LR or RL,corresponding to horizontal layouts, the top-level fields are displayed vertically.

As an example of a record node, the dot input:

yields the figure:

If we add the line:

we get the layout:

If we change node struct1 to have shape Mrecord,it then looks like:

Styles for Nodes

The styleattribute can be used to modify the appearance of a node.At present, there are 8 style values recognized:filled, invisible, diagonals, rounded.dashed, dotted, solid and bold.As usual, the value of the styleattribute can be a comma-separated list of any of these. If thestyle contains conflicts (e.g, style='dotted, solid'), the lastattribute wins.

filled
This value indicates that the node’s interior should be filled.The color used is the node’s fillcolor or, if that’s not defined, itscolor. For unfilled nodes, the interior of the node is transparent towhatever color is the current graph or cluster background color.Note that point shapes are always filled.

Thus, the code:

yields the figure:

invisible
Setting this style causes the node not to be displayed at all.Note that the node is still used in laying out the graph.
diagonals
The diagonals style causes small chords to be drawn near the verticesof the node’s polygon or, in case of circles and ellipses, two chords nearthe top and the bottom of the shape. The special node shapesMsquare,Mcircle, andMdiamondare simply an ordinary square, circle anddiamond with the diagonals style set.
rounded
The rounded style causes the polygonal corners to be smoothed.Note that this style also applies to record-based nodes. Indeed,the Mrecord shape is simply shorthand for setting this style.Also, prior to 26 April 2005, the rounded and filled styles were mutually exclusive.

As an example of rounding, dot uses the graph:

to produce the figure:

Using Graphviz In Python

Graphviz
dashed
This style causes the node’s border to be drawn as a dashed line.
dotted
This style causes the node’s border to be drawn as a dotted line.
solid
This style causes the node’s border to be drawn as a solid line,which is the default.
bold
This style causes the node’s border to be drawn as a bold line.See also penwidth.

Additional styles may be available with a specific code generator.

HTML-Like Labels

NOTE: This feature is only available on versions of Graphvizthat are newer than mid-November 2003. In particular, it is not partof release 1.10.

NOTE: The font markups for bold, italic, underlining, subscript and superscript (<B>, <I>, <U>, <SUB> and <SUP>) are only available in versions after 14 October 2011, and the markup for strike-through (<S>) requires versions later than 15 September 2013.In addition, all of these markups arecurrently only available via the cairo and svg renderers.The horizontal and vertical rules (<HR> and <VR>)are only available in versions later than 8 July 2011.

NOTE: For releases later than 9 September 2014, one can use shape=plain so that the sizeof the node is totally determined by the label. Otherwise, the node’s margin, width and height values may cause thenode to be larger, so that edges are clipped away from the label. In effect, shape=plain is shorthandfor shape=none width=0 height=0 margin=0.

If the value of a label attribute(label for nodes, edges, clusters, andgraphs, and theheadlabel andtaillabelattributes of an edge) is given as anHTML string,that is, delimited by <...>rather than '...',the label is interpreted asan HTML description. At their simplest, such labelscan describe multiple lines of variously aligned text as provided by ordinary string labels. More generally, thelabel can specify a table similar to those provided by HTML,with different graphical attributes at each level.

As HTML strings are processed like HTML input, any use ofthe ', &, <, and > characters in literal text or in attribute valuesneed to be replaced by the corresponding escape sequence. For example, if you want touse & in an href value, this should be represented as &amp;.

NOTE: The features and syntax supported by these labels aremodeled on HTML. However, there are many aspects that are relevantto Graphviz labels that are not in HTML and, conversely, HTML allowsvarious constructs which are meaningless in Graphviz. We will generallyrefer to these labels as “HTML labels” rather than the cumbersome“HTML-like labels” but the reader is warned that these are not reallyHTML. The grammar below describes precisely what Graphviz will accept.

Although HTML labels are not, strictly speaking, a shape, they can beviewed as a generalization of the record shapes described above. In particular, if a node has set its shapeattribute to none or plaintext, the HTML label will be the node’sshape. On the other hand, if the node has any other shape (except point), the HTML label will be embedded within the node thesame way an ordinary label would be. Adding HTML labels to record-based shapes (record and Mrecord) is discouraged and may lead to unexpected behavior because of their conflicting label schemas and overlapping functionality.

The following is an abstract grammar for HTML labels.Terminals, corresponding to elements, are shown in bold font,and nonterminals in italics.Square brackets [ and ] enclose optional items.Vertical bars separate alternatives.Note that, as in HTML, element and attribute names are case-insensitive.(cf. sections 3.2.1 and 3.2.2 of the HTML 4.01 specification).

label:text
fonttable
text:textitem
texttextitem
textitem:string
<BR/>
<FONT>text</FONT>
<I>text</I>
<B>text</B>
<U>text</U>
<O>text</O>
<SUB>text</SUB>
<SUP>text</SUP>
<S>text</S>
fonttable:table
<FONT>table</FONT>
<I>table</I>
<B>table</B>
<U>table</U>
<O>table</O>
table:<TABLE>rows</TABLE>
rows:row
rowsrow
rows<HR/>row
row:<TR>cells</TR>
cells:cell
cellscell
cells<VR/>cell
cell:<TD>label</TD>
<TD><IMG/></TD>

All non-printing characters such as tabs or newlines are ignored.Above, a string is any collection of printable characters, includingspaces. For tables, outside of the body of a <TD> element,whitespace characters are ignored, including spaces; within a <TD> element, spacesare preserved but all other white space characters are discarded.N.B. For technical reasons, if a table is wrapped in a font element such as <FONT>or <B>, any space immediately before or after this will cause a syntax error. For example,the label

is not legal. Removing either the space or the <U>...</U> will fix this.

HTML comments are allowed within an HTML string. They can occur anywhereprovided that, if they contain part of an HTML element, they must containthe entire element.

As is obvious from the above description, the interpretation of white spacecharacters is one place where HTML-like labels is very different from standard HTML. In HTML, any sequence of white space characters is collapsed to a single space, If the user does not want this to happen, theinput must use non-breaking spaces &nbsp;. This makes sense inHTML, where text layout depends dynamically on the space available. InGraphviz, the layout is statically determined by the input, so it isreasonable to treat ordinary space characters as non-breaking. In addition,ignoring tabs and newlines allows the input text to be formatted foreasier reading.

Each of the HTML elements has a set of optional attributes.Attribute values must appear in double quotes.

Table element
Table row
Table cell
Font specification
Line break
Image inclusion
Italic style
Bold style
Underline text
Overline text
Subscript text
Superscript text
Strike-through text
Horizontal rule
Vertical rule
ALIGN
specifies horizontal placement. When an object is allocatedmore space than required, this value determines where the extra spaceis placed left and right of the object.
  • CENTER aligns the object in the center. (Default)
  • LEFT aligns the object on the left.
  • RIGHT aligns the object on the right.
  • (<TD> only) TEXT aligns lines of text using the full cell width. The alignment of a line is determined by its (possibly implicit) associated <BR> element.

The contents of a cell are normally aligned as a block. In particular,lines of text are first aligned as a text block based on the width ofthe widest line and the corresponding <BR> elements. Then,the entire text block is aligned within a cell. If, however, thecell’s ALIGN value is TEXT, and the cell containslines of text, then the lines are justified using the entire availablewidth of the cell. If the cell does not contain text, then the containedimage or table is centered.

BALIGN
specifies the default alignment of <BR> elements containedin the cell. That is, if a <BR> element has noexplicit ALIGN attribute, the attribute value is specifiedby the value of BALIGN.
Svg
BGCOLOR=”color”
sets the color of the background. This color can be overridden by a BGCOLOR attribute in descendents.The value can be a single color or two colors separated by a colon, thelatter indicating a gradient fill.
BORDER=”value”
specifies the width of the border around the object in points.A value of zero indicates no border. The default is 1.The maximum value is 255.If set in a table, and CELLBORDER is not set,this value is also used for all cells in the table.It can be overridden by a BORDER attribute in a cell.
CELLBORDER=”value”
specifies the width of the border for all cells in a table.It can be overridden by a BORDER tag in a cell.The maximum value is 255.
CELLPADDING=”value”
specifies the space, in points, between a cell’s border and its content.The default is 2.The maximum value is 255.
CELLSPACING=”value”
specifies the space, in points, between cells in a table and betweena cell and the table’s border. The default is 2.The maximum value is 127.
COLOR=”color”
sets the color of the font within the scope of<FONT>...</FONT>, or the border colorof the table or cell within the scope of<TABLE>...</TABLE>,or <TD>...</TD>.This color can be overridden by a COLOR attribute in descendents.By default, the font color is determined by thefontcolor attribute ofthe corresponding node, edge or graph, and the border coloris determined by thecolor attribute ofthe corresponding node, edge or graph.
COLSPAN=”value”
specifies the number of columns spanned by the cell. The default is 1.The maximum value is 65535.
COLUMNS=”value”
provides general formatting information concerning the columns.At present, the only legal value is *, which causes a vertical rule toappear between every cell in every row.
FACE=”fontname”
specifies the font to use within the scope of<FONT>...</FONT>.This can be overridden by a FACE attribute in descendents.By default, the font name is determined by thefontname attribute of the correspondingnode, edge or graph.
FIXEDSIZE
specifies whether the values given by the WIDTHand HEIGHT attributes are enforced.

Graphviz Python Show

  • FALSE allows the object to grow so that all its contents will fit. (Default)
  • TRUE fixes the object size to its given WIDTH and HEIGHT. Both of these attributes must be supplied.
GRADIENTANGLE=”value”
gives the angle used in a gradient fill if the BGCOLOR is a color list. For the default linear gradient,this specifies the angle of a line through the center along which the colors transform.Thus, an angle of 0 will cause a left-to-right progression.For radial gradients (see STYLE), the angle specifies the positionof the center of the coloring. An angle of 0 places the center at the center of thetable or cell; an non-zero angle places the fill center along that angle near theboundary.
HEIGHT=”value”
specifies the mininum height, in points, of the object. The heightincludes the contents, any spacing and the border. UnlessFIXEDSIZE is true, the height will be expanded to allowthe contents to fit.The maximum value is 65535.
HREF=”value”
attaches a URL to the object.Note that the 'value' is treated as anescString similarly to theURL attribute.
ID=”value”
allows the user to specify a unique ID for a table or cell. Seethe id attribute for more information.Note that the 'value' is treated as anescString similarly to theid attribute.
POINT-SIZE=”value”
sets the size of the font, in points, used within the scope of<FONT>...</FONT>.This can be overridden by a POINT-SIZE attribute in descendents.By default, the font size is determined by thefontsize attribute of the correspondingnode, edge or graph.
PORT=”value”
attaches a portname to the object.(See portPos.)This can be used to modify the heador tail of an edge, so that the end attaches directly to the object.
ROWS=”value”
provides general formatting information concerning the rows.At present, the only legal value is *, which causes a horizontal rule toappear between every row.
ROWSPAN=”value”
specifies the number of rows spanned by the cell. The default is 1.The maximum value is 65535.
SCALE
specifies how an image will use any extra space available in its cell.Allowed values are
  • FALSE : keep image its natural size. (Default)
  • TRUE : scale image uniformly to fit.
  • WIDTH : expand image width to fill
  • HEIGHT : expand image height to fill
  • BOTH : expand both image width height to fillIf this attribute is undefined, the image inherits the imagescaleattribute of the graph object being drawn.As with the imagescaleattribute, if the cell has a fixed size and the image is too large,any offending dimension will be shrunk to fit the space, thescaling being uniform in width and height if SCALE='true'.Note that the containing cell’s ALIGNand VALIGN attributes overridean image’s SCALE attribute.
SIDES=”value”
specifies which sides of a border in a cell or table should be drawn, ifa border is drawn. By default, all sides are drawn. The 'value'string can contain any collection of the (case-insensitive) characters 'L', 'T', 'R', or 'B',corresponding to the left, top, right and, bottom sides of the border,respectively. For example, SIDES='LB' would indicate only theleft and bottom segments of the border should be drawn.
SRC=”value”
specifies the image file to be displayed in the cell.Note that if the software is used as a web server, file system accessto images is more restricted. See GV_FILE_PATHand SERVER_NAME.
STYLE
specifies style characteristics of the table or cell. Style characteristics aregiven as a comma or space separated list of style attributes. At present, the onlylegal attributes are ROUNDED and RADIAL for tables, and RADIAL for cells.If ROUNDED is specified, the table will have rounded corners.This probably works best if the outmost cells have no borders, or their CELLSPACINGGraphviz python renderis sufficiently large.If it is desirable to have borders around the cells, use HRand VR elements, or the COLUMNS and PythonROWS attributes of TABLE.

The RADIAL attribute indicates a radial gradient fill. See the BGCOLOR andGRADIENTANGLE attributes.

TARGET=”value”
determines which window of the browser is used for the URL if the object has one. See W3C documentation.Note that the 'value' is treated as anescString similarly to thetarget attribute.
TITLE=”value”
sets the tooltip annotation attached to the element. This is used only if the element has a HREF attribute.Note that the 'value' is treated as anescString similarly to thetooltip attribute.
TOOLTIP=”value”
is an alias for TITLE.
Graphviz python render
VALIGN
specifies vertical placement. When an object is allocatedmore space than required, this value determines where the extra spaceis placed above and below the object.
  • MIDDLE aligns the object in the center. (Default)
  • BOTTOM aligns the object on the bottom.
  • TOP aligns the object on the top.
WIDTH=”value”
specifies the mininum width, in points, of the object. The widthincludes the contents, any spacing and the border. UnlessFIXEDSIZE is true, the width will be expanded to allowthe contents to fit.The maximum value is 65535.

There is some inheritance among the attributes. If a table specifiesa CELLPADDING, CELLBORDER or BORDERvalue, this value is used by the table’scells unless overridden. If a cell or table specifies a BGCOLOR,this will be the background color for all of its descendents.Of course, if a background or fill color is specified for thegraph object owning the label, this will be the originalbackground for the label.The object’s fontname, fontcolor and fontsize attributesare the default for drawing text. These can be overridden by usingFONT to set new values. The new font values will holduntil overridden by an enclosed FONT element.Finally, the pencolor or color of the graph object will be used asthe border color.

Graphviz Python Save Image

If you want horizontal or vertical rules used uniformly within a table, considerusing the COLUMNS or ROWS attributesrather than using manyHR and VR elements.

Because of certain limitations in handling tables in a device-independentmanner, when BORDER is 1 and both table and cell bordersare on and CELLSPACING is less than 2, anomalies can arisein the output, such as gaps between sides of borders which should beabutting or even collinear. The user can usual get around this by increasingthe border size or the spacing, or turning off the table border.

HTML-Like Label Examples

Recreating the Record Example

The dot input:

produces the HTML analogue of the record example above:

As usual, an HTML specification is more verbose.

More Complex Example

On the other hand, HTML labels are much more general:

produces:

Fonts Example

An example using <FONT> elements:

produces:

Images Example

Using an <IMG> element:

produces:

Sides Example

The sides attribute (version 2.37 and later) allows one to combine cells to formvarious non-convex shapes. For example, a tee-shaped node

produces:

User-defined Node Shapes

There is a third type of node shape which is specified by the user.Typically, these shapes rely on the details of a concrete graphicsformat. At present, shapes can be described using PostScript, via afile or add-on library, for use in PostScript output, or shapes canbe specified by a bitmap-image file for use with SVG or bitmap (jpeg,gif, etc.) output. More information can be found on the page How to create custom shapes.

SDL Shapes for PostScript

One example of user-defined node shapes is provided by Mark Rison of CSR.These are the SDL shapes.These are available as PostScript functions whose use is described inExternal PostScript procedures.The necessary PostScript library file and sample use can be found in thecontrib/sdlshapes directory in the release. Please note theCOPYRIGHT AND PERMISSION NOTICE contained in the library file sdl.ps.

The table belowgives the shape names and the corresponding node shapes: