SMITIDvisu (version 0.0.9)

Visualize Data for Host and Viral Population from 'SMITIDstruct' using 'HTMLwidgets'

Description

Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using 'HTMLwidgets'. It mainly using 'D3JS' javascript framework.

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Version

Install

install.packages('SMITIDvisu')

Monthly Downloads

184

Version

0.0.9

License

GPL (>= 3) | file LICENSE

Homepage

https://informatique-mia.inrae.fr/biosp/anr-smitid-project/

Maintainer

Jean-Francois Rey

Last Published

February 8th, 2021

Functions in SMITIDvisu (0.0.9)

updateTransmissionTree

timeLineProxy

timeLineProxy get an instance of a timeline

tt.events

Data.frame of hosts events information by time. Fake data.

demo.SMITIDvisu.run

tt.edges

Pathogen link over the time

st.dist113_all

Distance matrix of observed variants sequences of a host 113 at time 2, 3 and 4 from simulation.

A SMITIDstruct package variable.

st.listTimeProp113

List of variants ID with subvector for time and value.

transmissionTree

st.dist113_2

Distance matrix of observed variants sequences of a host 113 at time 2 from simulation.

st.prop113_2

Variants proportions and count for host 113 at time 2 from simulation.

updateTimeLine

tt.nodes

Host list with there status over the time.

st.prop113_all

Variants proportions and count for an host 113 at time 2, 3 and 4 from simulation.

transmissionTreeProxy

df2geojson

createRainbowColors

createRainbowColors Create a list of colors for each value v

SMITIDvisu-shiny

Shiny bindings for visualisation widgets

SMITIDvisu-package

Visualize Data for Host and Viral Population from SMITIDstruct using HTMLwidgets

hostline

A host infomation over time

compute the minimum spanning tree