Package 'SMITIDvisu'

Title: 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.
Authors: Jean-Francois Rey [aut, cre], Julien Boge [ctb]
Maintainer: Jean-Francois Rey <[email protected]>
License: GPL (>= 3) | file LICENSE
Version: 0.0.9
Built: 2024-12-19 06:24:48 UTC
Source: https://github.com/cran/SMITIDvisu

Help Index

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

Package: SMITIDvisu
Type: Package
Version: 0.0.9
Date: 2021-02-08
License: GPL (>=3)

Author(s)

Jean-Francois Rey [email protected]

Julien Boge [email protected]

Examples

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

## End(Not run)

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

v

a vector of characters

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

df

Data frame to convert in GeoJSON. It must contain at least columns 'id', 'time', 'X' and 'Y'. Additionnal columns will be added as features' properties.
multipleValuesByTime

Vector of strings indicating the df columns names which can contain several values by time.

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

data

Either a data frame that will be converted to a GeoJSON collection, or a string describing a valid GeoJSON collection. The data frame must contain at least columns 'id', 'time', 'X' and 'Y'. It can contain columns 'infectedby', 'probabilities'. Additionnal columns will be added as properties, but will do nothing in this implementation of maptt. See the 'df2geojson' function for more informations.
multipleValuesByTime

Vector of strings indicating the df columns names which can contain several values by time. Typically, you would use ‘c(’infectedby','probabilities')' if you have these values.
circleRadius

Numeric value specifying the radius of the nodes in pixels.
defaultNodeColor

String indicating the default color of nodes, if their status doesn't match whith any color. Colors can be specified in hex.
nodeColorByState

List of strings, indicating the color scheme for each node state.
moveEdgeColor

String indicating the color of the edges representing the move of a node.
color1

String indicating the color corresponding to the minWeight value.
color2

String indicating the color corresponding to the maxWeight value.
nbColors

Number of colors for the color scheme using a gradient between color1 and color2. These colors will be used to represent the infection edges according to the infection probability. If no probability is used, the edge will use color2. Three intervals are created : color1 will be used for the probabilities between minWeight and weight1. Colors between color1 and color2 will be used for probabilities between weight1 and weight2. color2 will be used for probabilities between weight2 and maxWeight. This setting can be modified directly on the map if 'gradientControl' is activated.
minWeight

Minimal weight.
maxWeight

Maximal weight.
weight1

Lowest weight for the color scheme. This setting can be modified directly on the map if 'gradientControl' is activated.
weight2

Greatest weight for the color scheme. This setting can be modified directly on the map if 'gradientControl' is activated.
autoFocus

Boolean indicating if the map should focus at the displayed features at each time. This setting can be toggled directly on the map if 'optionsControl' is activated.
keepOldFeatures

Boolean indicating if old features should be displayed or not. Features are considered "old" if their last 'time' is prior to the current time displayed. This setting can be toggled directly on the map if 'optionsControl' is activated.
optionsControl

Boolean indicating if the options control should be displayed or not
gradientControl

Boolean indicating if the gradient control should be displayed or not
legend

Boolean indicating if the legend should be displayed or not
width

Numeric width for the area in pixels.
height

Numeric hieght for the area in pixels.
elementId

The element ID where the map is displayed

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

mapttId

widget instance identifier
session

shiny session

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

mapttProxy

mapttProxy instance
hostId

the id of the host to select

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

mat

weighted matrix representing nodes connection (edges weight)

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

mat

a distance matrix between sequence of variants (interger distance no floating values)
prop

a data.frame for variants sequences proportions and count (see details)
node.prop

list of variants with proportions and time (default NULL)
width

numeric width for the area in pixels.
height

numeric hieght for the area in pixels.
elementId

the element ID where is draw

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

mstVid

widget instance identifier
session

shiny session

Examples

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

## 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

outputId

output variable to read from
width, height

Must be a valid CSS unit (like "100%", "400px", "auto") or a number, which will be coerced to a string and have "px" appended.
expr

An expression that generates a networkD3 graph
env

The environment in which to evaluate expr.
quoted

Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

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

data

a data.frame that reprensent hosts status in time with ID, status and time in columns
title

a tttle as character
color

list of color for timeline elements
width

numeric width for the area in pixels.
height

numeric hieght for the area in pixels.
elementId

the element ID where is draw

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

tlid

a timeline instance id
session

shiny session

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

nodes

a data.frame that reprensent hosts status in time with ID, status and time in columns
edges

a data.frame that reprensent tramsmission link between hosts (pathogens) with ID, source, target and time in columns
nodes.color

a list of color for nodes status "status"="color"
width

numeric width for the area in pixels.
height

numeric hieght for the area in pixels.
elementId

the element ID where is draw

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

ttid

widget instance identifier
session

shiny session

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)

updatemstVariant

Description

update (redraw) an instance on mstVariant

Usage

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

Arguments

mstVProxy

mstVaraintProxy instance
mat

distance matrix
prop

proportions data.frame
propTime

list of each variant by time and proportions

See Also

mstVariant

Examples

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

## End(Not run)

updateTimeLine

Description

updateTimeLine

Usage

updateTimeLine(tlProxy, data, title)

Arguments

tlProxy

a timeline proxy instance
data

new data
title

new title

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

TTProxy

transmissionTreeProxy instance
nodes

a data.frame that represent hosts status in time with ID, status and time in columns
edges

a data.frame that represent tramsmission link between hosts (pathogens) with ID, source, weight, target and time in columns
options

transmissionTree new options

See Also

transmissionTree

Examples

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

## End(Not run)