pynteractive package

Submodules

pynteractive.datastruct module

class pynteractive.datastruct.DataStruct(name=None)

DataStruct is the basic data structure aimed to abstract any data set that will be represented in Pynteractive Web GUI. All different dataset inherit from DataStruct class, and datastruct class implements the basic mechanisms to communicate with the Pynteractive web server

addAction(name, func)

Actions can be added to each visualization

An action consists of a label (name) shown in the web interface plus a callback method (func) called then the button associated to the label is clicked. The callback function must accept one parameter that depending on the visualization can be defferent (eg. list of nodes, sample id, etc...)

example:

a=Graph()
def myfunc(nodes):
     print 'these are the selected nodes',nodes

a.addAction('Print selected nodes',myfunc)
a.view()

# Now you can select some nodes in the GUI and click your action on the left side bar

clearLog()

Clears the contents of the log box in the web GUI

closeView()

Closes the browser window/tab containing the dataset GUI

log(log)

Dumps HTML code in the Log section in the web GUI

static readCsv(csvfile)

readsCsv and returns the output as a vector of vectors. Detects delimiter automatically

selectionHandler(func)

Sets a hook method that will be fired every time a selection is performed

setDoubleClick(f)

Sets a callback as a response to a double click event on a graph node

view()

This method opens the default web browser in the system showing the web visualization associated to the data

pynteractive.Network module

class pynteractive.Network.Network(name=None, directed=False)

Bases: pynteractive.datastruct.DataStruct

This class implements basic methods and datastructures to represent a Newtork. IT is used for either Graphs or trees

addEdge(n1, n2, label, **kwargs)

Adds an edge from node n1 to node n2, if it is not directed the order does not matter. The edge id will be a combination of n1,n2 and label (eg: addEdge(‘node1’,’node2’,’connection_node1_node2’) –> edge_id = ‘node1~node2~connection_node1_node2’)

addNode(node_id=None, label=None, **kwargs)

Ads a node into the network, you can specify a cwnode_id and a label, if no node_id is specified, it will be randomly generated (autoincremental id) and if label is None it will get the same value as the node_id

Random parameters can be assigned to the node via **kargs.

It returns the tuple node_id,label.

delEdge(_id)

Deletes a connection between two given nodes

delNode(node_id)

Deletes a node from the network as well as the edges

getEdges()

Returns the edges of the Network –> ([edge_ids])

getNodes()

Returns the nodes of the Network –> ([node_ids])

updateNode(node_id, **kwargs)

Updates parameters related to node node_id updating those parameters specified via **kwargs

pynteractive.visNetwork module

class pynteractive.visNetwork.VisNetwork(name=None, directed=False)

Bases: pynteractive.Network.Network

addEdge(n1, n2, label=None, title=None, width=None, style=None, length=None)

Adds an edge to a node, if it is not directed the order does not matter:

• label: label on the edge
• title: text shown when hovering the edge
• width: width in pixeld of the edge
• style: line style -> line, arrow, arrow-center, dash-line
• length: length of the edge

addNode(node_id=None, label=None, title=None, group=None, shape='ellipse', color=None, radius=None, image=None)

Adds a node to the network:

• node_id: identification of the node, if not specified it will be randomly generated
• label: Text that will be shown within the node
• title: Tooltip shown when hovering the node
• group: color group (numeric, eg: 1,2,3,4) used for clusterings
• shape: any of ellipse, circle, box, database, image, circularImage, label, dot, star, triangle, triangleDown, square
• color: color name or html code (eg: red, #FF0000)
• radius: radius of the shape
• image: Image in case the shape is image or circularImage

clear()

Clears the GUI by removing every node and edge in the network

delEdge(ed_id)

Deletes a connection between two given nodes

delNode(node_id)

Deletes a node from the network as well as the edges

focusNode(id)

Forces the GUI to zoom in into the specified node

updateNode(node_id, label=None, title=None, group=None, shape=None, color=None, radius=None, image=None)

Updates a node in the network

pynteractive.graph module

class pynteractive.graph.Graph(name=None, directed=False)

Bases: pynteractive.visNetwork.VisNetwork

fromCsv(fil, matrix=False, distances=False)

Draws a network given a csv file

The format for the CSV can be:

Pair of nodes connected

n1	n2
a	b
a	c
c	d

Node in first column connected to the ones in the next columns

n1	n2
a	b	d	e
b	c	e
e	f	a	d	e

Network matrix (matrix=True,distances=False)

	a	b	c	d	e	f
a	1	0	0	0	0	0
b	1	0	0	0	0	0
c	0	1	1	1	0	0
d	0	1	0	0	1	0
e	1	0	0	0	1	1
f	0	0	0	0	1	1

Network matrix with distances (matrix=True,distances=True)

	a	b	c	d	e	f
a	54	0	0	0	0	0
b	23	0	0	0	0	0
c	0	10	2	1	0	0
d	0	10	0	0	13	0
e	56	0	0	0	1	1
f	0	0	0	0	3	1

random(nn, ne)

Creates a random Graph containing nn nodes and ne edges

pynteractive.map module

class pynteractive.map.Map(name=None)

Bases: pynteractive.Network.Network

The Map class allows to plot data in an OpenStreet Map. The user can plot points of different sizes and colors as well as linking them with edges. In order to specify the location coordinates or places (eg. postcode) can be used.

CACHE = {}

LOCK = <thread.lock object>

MAXTHREADS = 15

RUNNINGTHREADS = <threading._Semaphore object>

THREADS = []

addEdge(n1, n2, color='red', width=2)

Ads and edge between two points given a color tag

addNode(*args, **kwargs)

clear()

Deletes all the information plotted in the map

delEdge(eid)

Deletes an edge given an egde ID

delNode(node_id)

Deletes a node from the map

focusNode(node_id)

Zooms into a given node

updateNode(node_id, radius=None, color=None, lng=None, lat=None, place=None, country=None)

Updates a node in the Map

pynteractive.tree module

class pynteractive.tree.Tree(name=None, directed=None)

Bases: pynteractive.Network.Network

getName(name)

readNewick(newick)

pynteractive.chart module

class pynteractive.chart.Chart(name=None, type='line')

Bases: pynteractive.datastruct.DataStruct

SHAPES = set(['triangle-down', 'diamond', 'cross', 'triangle-up', 'square', 'circle'])

TYPES = {'line': 'Line', 'bar': 'Bar', 'scatter': 'Scatter', 'stack': 'Stack'}

addSeries(seriesName, x=[], y=[], sizes=[], shapes=[], data=[], csv=None)

Adds a series of data. A series of data has to have a name and a collection of (x,y) pairs that can be either integers or floats

if the chart is a scatter you can add as well sizes and or shapes.

The available shapes are: ‘circle’, ‘cross’, ‘triangle-up’, ‘triangle-down’, ‘diamond’, ‘square’

There are several ways of adding data:

a=Chart()
a.addSeries('dataset1',[1,2,3],[4,5,6])
a.addSeries('dataset2',[1,2,3],[4,5,6],sizes=[.5,.5,.2],shapes=['circle','cross','square'])
a.addSeries('dataset3',data=[[1,4],[2,5],[3,6]])
a.addSeries('dataset4',data=[[1,4,.5,'circle'],[2,5,.5,'cross'],[3,6,.2,'square']])
a.addSeries('dataset5',csv='file.csv') # The format has to the same as we pass it to data parameter

addValue(idSeries, x, y, **kwargs)

Ads a value into a series, extra parameters can be size=N and shape=’XXX’

changeType(type)

Changes the chart type in the view, the following types are available: ‘bar’,’scatter’,’line’,’stack’

delSeries(seriesName)

Deletes a series from the graph

delValue(idSeries, x)

Deletes a value from a series

pynteractive.phylotree module

class pynteractive.phylotree.PhyloTree(name=None)

Bases: pynteractive.datastruct.DataStruct

addBar(description, color, minval, maxval)

Outside the tracks, bars can be drawn showing extra information. You can have as many bars you want per sector (tip) (eg: if you want two bars in a barplot per tip, you call addBar twice and then you populate them with data

• description: Text description for the legend

• color: color used for the bar

• minval: minimum value of the data that the bars will show

• maxval: maximum value of the data that the bars will show

  Returns the Bar identifier to be used to add data to it (See example below)

addGradientTrack(description, color, minval, maxval)

A gradient Track is a track where tips in the tree can have a continuous value, and the color will be shown as a gradient color. You must specify minval and maxval of the track so that the gradient can be calculated

• description: Text used for the legend

• color: color used for the gradient on track

• minval: Minimum value of the range of values this track will have

• maxval: Minimum value of the range of values this track will have

  Returns the track ID that you will have to use to add data to it

addMultiColorTrack(description, colordict)

A Multicolor track is a track that can have random colors given a color dictionary eg: {“uk”:’red’,”france”:’green’,”germany”:”#a2a2a2”} - description: Text used for the legend - colordict: Dictionary mapping values to colors

Returns the track ID that you will have to use to add data to it

addTrack(description, color)

Ads a track as an external ring. This is a BOOLEAN track, where any tip can be flagged in the track. When clicking a coloured tip on the track, all the tips flagged in the track will automatically be selected

• description: Text used for the legend

• color: color used for the flagged tips on the track

  Returns the track ID that you will have to use to add data to it

addTrackBar(nbar, tipname, value)

Adds data to a bar

• nbar: bar ID provided by addBar function
• tipname: name of the tip you will add data to
• value: Value the the bar will show

p=PhyloTree()
p.setData("file.newick")
contaminationBars=p.addBar('contamination','green',0,28)
p.addTrackBar(contaminationBars,'sample1',4)
p.addTrackBar(contaminationBars,'sample2',22)
p.addTrackBar(contaminationBars,'sample3',17) 

addTrackFeature(trackn, tipname, value=False, title=None)

Adds a data to a track:

• trackn: Track number to add data to
• tipname: The tip you want to add the feature to
• value: Only required/necessary if it’s a gradient track
• title: Tooltip shown when hovering with the mouse

p=PhyloTree()
p.setData("file.newick")
resistanteTrack=p.addTrack('Antibiotic resistante','red')
coverageTrack=p.addTrack('Avg Depth coverage','blue',0,344)
p.addTrackFeature(resistanceTrack,'sample1')
p.addTrackFeature(resistanceTrack,'sample3')
p.addTrackFeature(coverageTrack,'sampler1',25)
p.addTrackFeature(coverageTrack,'sampler2',221)
p.addTrackFeature(coverageTrack,'sampler3',344) 

clearBars()

Clears all bars around the tracks

clearCladeColor(clade)

Clears tree color given a clade

clearCladeMarks()

Removes all clade marks

clearSelection()

Method to clear the current selection in the tree

clearTracks()

Clears all information in tracks

delTrackFeature(trackn, tipname)

Deletes a feature present on a track

getTips()

Returns a set containing all the tip names found in the tree

markClade(nodes, color)

Marks the region of a clade given a fill color

• nodes: Is a list of tips/internalnodes
• color: HTML compatible color

nodeClick(nid)

Method called when a node is clicked

recolor = <_sre.SRE_Pattern object>

selectClade(tips)

Select the clade containing a set of given tips

selectTips(tips)

Method usd to select nodes in the view (tree tips), you must provide tip labels

setCladeColor(nodes, color)

Sets tree color for a clade

• nodes: Is a list of tips/internalnodes
• color: HTML compatible color

setData(newick=None)

Draws the specified newick tree, It can be either a string containing the newick string or a path to a file

unMarkClade(clade)

Removes a mark for a clade