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, noUiSlider and FileSaver javascript libraries.

Details

Author(s)

Jean-Francois Rey jean-francois.rey@inrae.fr

Julien Boge julien.boge.u@gmail.com

Examples

## Not run: 
 library(SMITIDvisu)
 demo.SMITIDvisu.run()

## End(Not run)

Shiny bindings for visualisation widgets

Description

Output and render functions for using visualisation widgets within Shiny applications and interactive Rmd documents.

Usage

mapttOutput(outputId, width = "100%", height = "400px")

renderMaptt(expr, env = parent.frame(), quoted = FALSE)

mstVariantOutput(outputId, width = "100%", height = "600px")

rendermstVariant(expr, env = parent.frame(), quoted = FALSE)

timeLineOutput(outputId, width = "100%", height = "400px")

renderTimeLine(expr, env = parent.frame(), quoted = FALSE)

transmissionTreeOutput(outputId, width = "100%", height = "500px")

renderTransmissionTree(expr, env = parent.frame(), quoted = FALSE)

Arguments

createRainbowColors Create a list of colors for each value v

Description

createRainbowColors Create a list of colors for each value v

Usage

createRainbowColors(v)

Arguments

Value

a list of value=color

demo.SMITIDvisu.run

Description

run a demo to visualize data

Usage

demo.SMITIDvisu.run()

df2geojson

Description

Transform a data frame into a string formatted in GeoJSON

Usage

df2geojson(df, multipleValuesByTime = c())

Arguments

Value

a geojson string

Examples

library(SMITIDvisu)
data(transmissiontree)
geojson <- df2geojson(tt.events, multipleValuesByTime = c('infectedby', 'probabilities'))

A host infomation over time

Description

kind of host time line

Usage

data("hostline")

Format

A data frame with 8 observations on the following 5 variables.

level

a character vector

label

a character vector

ID

a character vector

timestart

a character vector

timeend

a character vector

Examples

data(hostline)
print(hostline)

maptt

Description

Display a Transmission Tree over a map.

Usage

maptt(
  data,
  multipleValuesByTime = c(),
  circleRadius = 6,
  defaultNodeColor = "steelblue",
  nodeColorByState = list(),
  moveEdgeColor = "steelblue",
  color1 = "green",
  color2 = "red",
  nbColors = 10,
  minWeight = 0,
  maxWeight = 1,
  weight1 = 0,
  weight2 = 1,
  autoFocus = TRUE,
  keepOldFeatures = TRUE,
  optionsControl = TRUE,
  gradientControl = TRUE,
  legend = TRUE,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

Examples

library(SMITIDvisu)
data(transmissiontree)

maptt(tt.events, multipleValuesByTime = c('infectedby', 'probabilities'))

# In this example:
# - values lower than 20 will be yellow ;
# - values between 20 and 25 will use colors between yellow and red ;
# - values greater than 25 will be red.
maptt(tt.events,
 multipleValuesByTime = c('infectedby', 'probabilities'),
 color1 = 'yellow',
 color2 = 'red',
 nbColors = 10,
 minWeight = 0,
 maxWeight = 30,
 weight1 = 20,
 weight2 = 25
)

mapttProxy

Description

get mapttProxy

Usage

mapttProxy(mapttId, session = shiny::getDefaultReactiveDomain())

Arguments

Examples

## Not run: 
library(SMITIDvisu)
## server.R
mapttProxy <- mapttProxyProxy("mapttOutput")

## End(Not run)

mapttSelectHost

Description

select a host on a MapTT instance

Usage

mapttSelectHost(mapttProxy, hostId)

Arguments

See Also

maptt

Examples

## Not run: 
library(SMITIDvisu)
data(transmissiontree)
## server.R
mapttProxy("mapttOutput") %>% mapttSelectHost()

## End(Not run)

compute the minimum spanning tree

Description

compute the minimum spanning tree of a matrix representing edges between nodes (of a graph)

Usage

mstCompute(mat)

Arguments

Value

a matrix with 1 if nodes are linked, 0 otherwise.

mstVariant

Description

Draw Variants genotypes distances as a graph using Minimum Spanning Tree algorithm.

Usage

mstVariant(
  mat,
  prop,
  node.prop = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

Details

mat is a simple distance matrix with interger values, row and lines contain a unique identifier of each variant sequences. prop is a data.frame where each row is a variant sequence, it have to contain in columns factor "ID", "proportion" and "count". "ID" is a unique identifier matching matrix value identifier, "proportion" is the proportions of the variant sequence and "count" the number of variant sequence in a varions set. node.prop is a list with name that matching mat identifier and prop "ID". Each list element contains a subvector time (Julian or timestamp) and value (proportions). That allow to draw variants proportions over time.

Examples

library(SMITIDvisu)
data(st)
mstV <- mstVariant(st.dist113_all,st.prop113_all, st.listTimeProp113)
## Not run:  
## export as standalone html file
htmlwidgets::saveWidget(mstV, "mstVariant.html")
browseURL("mstVariant.html")

## End(Not run)

mstVariantProxy

Description

get mstVariantProxy

Usage

mstVariantProxy(mstVid, session = shiny::getDefaultReactiveDomain())

Arguments

Examples

## Not run: 
library(SMITIDvisu)
## server.R
mstVariantProxy <- mstVaraintProxy("mstvariantoutput")

## End(Not run)

A SMITIDstruct package variable.

Description

A SMITIDstruct package variable from simul-chain as a list. The list is a set of HostSet, ViralPopset and an index

Usage

data("st")

Format

The format is: List of 3 $ :List of 21 .. ..- attr(*, "class")= chr "HostSet" $ :List of 20 .. ..- attr(*, "class")= chr "ViralPopSet" $ :'data.frame': 79 obs. of 3 variables: ..$ TIME : chr [1:79] "0" "0" "1.26" "1.35" ... ..$ ID_HOST : chr [1:79] "1" "2" "2" "2" ... ..$ EVENTCODE: chr [1:79] "000011" "000110" "001000" "001000" ...

Examples

data(st)
## maybe str(st) ; plot(st) ...

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

Description

Levenshtein Distance matrix with rows and cols label as sequences ID.

Usage

data("st")

Format

The format is: num [1:23, 1:23] 0 1 1 1 2 1 1 1 1 2 ...

Examples

data(st)

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

Description

Levenshtein Distance matrix with rows and cols label as sequences ID. Unique sequence variants observed on host 113 at time 2, 3 and 4 from a simulation.

Usage

data("st")

Format

The format is: num [1:51, 1:51] 0 1 1 1 1 1 3 1 1 1 ...

Examples

data(st)

List of variants ID with subvector for time and value.

Description

A list indexed by variants sequences ID. Each element contain a time and value vector for time of observation and proportions observed at this time.

Usage

data("st")

Examples

data(st)

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

Description

A data.frame with label "ID", "proportion" and "count" for an host 113 at time 2 from simulation. Each row is a sequence.

Usage

data("st")

Format

A data frame with 23 observations on the following 3 variables.

ID

a character vector

proportion

a numeric vector

count

a numeric vector

Examples

data(st)

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

Description

A data.frame with label "ID", "proportion" and "count" for an host 113 at time 2, 3 and 4 from simulation. Each row is a sequence.

Usage

data("st")

Format

A data frame with 51 observations on the following 3 variables.

ID

a character vector

proportion

a numeric vector

count

a numeric vector

Examples

data(st)

timeLine

Description

Draw a host time line. Time use timestamp or Date in ISO format.

Usage

timeLine(
  data,
  title,
  color = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

Examples

library(SMITIDvisu)
data(hostline)
tl <- timeLine(hostline,
               title="Example host 113",
               color=list("infected"="red","offspring"="green",
                             "alive"="blue","inf"="orange",
                             "dead"="black","Obs"="purple"))
## Not run: 
## export as standalone html file
htmlwidgets::saveWidget(tl, "timeline.html")
browseURL("timeline.html")

## End(Not run)

timeLineProxy get an instance of a timeline

Description

timeLineProxy get an instance of a timeline

Usage

timeLineProxy(tlid, session = shiny::getDefaultReactiveDomain())

Arguments

Value

an object of class timeline_proxy

Examples

## Not run: 
## server.R
## output server variable
output$timeline <- renderTimeLine({
         timeLine(data.frame(), "")
       })
## ui.R
timeLineOutput("timeline")
## server.R
tlproxy <- timeLineProxy("timeline")

## End(Not run)

transmissionTree

Description

Draw a transmission tree over the time. Time use timestamp or Date in ISO format ("

Usage

transmissionTree(
  nodes,
  edges,
  nodes.color = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL
)

Arguments

Examples

library(SMITIDvisu)
data(transmissiontree)
tt <- transmissionTree(tt.nodes,tt.edges, nodes.color = list("default"="black","Inf"="red"))
## Not run: 
## export as standalone html file
htmlwidgets::saveWidget(tt, "transTree.html")
browseURL("transTree.html")

## End(Not run)

transmissionTreeProxy

Description

get transmissionTreeProxy

Usage

transmissionTreeProxy(ttid, session = shiny::getDefaultReactiveDomain())

Arguments

Examples

## Not run: 
library(SMITIDvisu)
## server.R
transmissionTreeProxy <- transmissionTreeProxyProxy("transmissionTreeoutput")

## End(Not run)

Pathogen link over the time

Description

A data.frame of all transmission links between hosts (pathogens). Five columns ID, source, target, time and weight.

Usage

data("transmissiontree")

Format

A data frame with 13 observations on the following 5 variables.

ID

a numeric vector

source

a character vector

target

a factor with levels 113 104 116 115 111 109 105 108 106 112

time

a character vector

weight

a character vector

Examples

data(transmissiontree)
print(tt.edges)

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

Description

Fake simulated data of hosts events over the time.

Usage

data("transmissiontree")

Format

A data frame with 63 observations on the following 7 variables.

id

a character vector

time

a character vector

status

a character vector

infectedby

a character vector

probabilities

a character vector

X

a numeric vector

Y

a numeric vector

Examples

data(transmissiontree)
print(tt.events)

Host list with there status over the time.

Description

a data.frame of all the hosts identify by there ID. Three colums is use ID, status and time

Usage

data("transmissiontree")

Format

A data frame with 47 observations on the following 3 variables.

ID

a character vector

status

a character vector

time

a character vector

Examples

data(transmissiontree)
print(tt.nodes)

updateTimeLine

Description

updateTimeLine

Usage

updateTimeLine(tlProxy, data, title)

Arguments

See Also

timeLine

Examples

## Not run: 
## server.R
## output server variable
output$timeline <- renderTimeLine({
         timeLine(data.frame(), "")
       })
## ui.R
timeLineOutput("timeline")
## server.R
timeLineProxy("timeline") %>% updateTimeLine(newtimeline, "newId")

## End(Not run)

updateTransmissionTree

Description

update (redraw) an instance of a transmissionTree

Usage

updateTransmissionTree(TTProxy, nodes, edges, options = NULL)

Arguments

See Also

transmissionTree

Examples

## Not run: 
library(SMITIDvisu)
data(transmissionTree)
## server.R
transmissionTreeProxy("transmissionTreeoutput") %>% updatetransmissionTree(tt.nodes,tt.edges)

## End(Not run)

updatemstVariant

Description

update (redraw) an instance on mstVariant

Usage

updatemstVariant(mstVProxy, mat, prop, propTime = NULL)

Arguments

See Also

mstVariant

Examples

## Not run: 
library(SMITIDvisu)
data(mstVariant)
## server.R
mstVaraintProxy("mstvariantoutput") %>% updatemstVariant(st.dist,st.prop)

## End(Not run)