The deploid-shinyapp from deploid-dev

url_content = "https://ndownloader.figshare.com/files/8916217?private_link=f09830a270360a4fe4a5"
library(RCurl)
myfile <- getURL(url_content)
plaf <- read.table(textConnection(myfile), header=T)
head(plaf)

plot wsaf using dygraph

dygraph
function (data, main = NULL, xlab = NULL, ylab = NULL, periodicity = NULL, 
    group = NULL, elementId = NULL, width = NULL, height = NULL) 
{
    if (xts::xtsible(data)) {
        if (!xts::is.xts(data)) 
            data <- xts::as.xts(data)
        format <- "date"
    }
    else if (is.list(data) && is.numeric(data[[1]])) {
        if (is.null(names(data))) 
            stop("For numeric values, 'data' must be a named list or data frame")
        format <- "numeric"
    }
    else {
        stop("Unsupported type passed to argument 'data'.")
    }
    if (format == "date") {
        if (is.null(periodicity)) {
            if (nrow(data) < 2) {
                periodicity <- defaultPeriodicity(data)
            }
            else {
                periodicity <- xts::periodicity(data)
            }
        }
        time <- time(data)
        data <- zoo::coredata(data)
        data <- unclass(as.data.frame(data))
        timeColumn <- list()
        timeColumn[[periodicity$label]] <- asISO8601Time(time)
        data <- append(timeColumn, data)
    }
    else {
        data <- as.list(data)
    }
    attrs <- list()
    attrs$title <- main
    attrs$xlabel <- xlab
    attrs$ylabel <- ylab
    attrs$labels <- names(data)
    attrs$legend <- "auto"
    attrs$retainDateWindow <- FALSE
    attrs$axes$x <- list()
    attrs$axes$x$pixelsPerLabel <- 60
    x <- list()
    x$attrs <- attrs
    x$scale <- if (format == "date") 
        periodicity$scale
    else NULL
    x$group <- group
    x$annotations <- list()
    x$shadings <- list()
    x$events <- list()
    x$format <- format
    attr(x, "time") <- if (format == "date") 
        time
    else NULL
    attr(x, "data") <- data
    attr(x, "autoSeries") <- 2
    names(data) <- NULL
    x$data <- data
    htmlwidgets::createWidget(name = "dygraphs", x = x, width = width, 
        height = height, htmlwidgets::sizingPolicy(viewer.padding = 10, 
            browser.fill = TRUE), elementId = elementId)
}

Change VCF Upload part to Tab “Sample Info"

Sample info

Tick boxes for choosing pv or pf
Given the choice of 1, dropdown list for choosing the origin of the file
Link to google map, show the plaf used individual origins

download gene annotation files for both pf and pv

plot gene annotations on the WSAF vs POS plot

DEploid-r compile on windows

read http://thecoatlessprofessor.com/programming/rcpp/install-rtools-for-rcpp/

pf country list

Africa

Malawi, Congo;
Ghana (Kassena);
Nigeria, Senegal, Mali;
Gambia, Guinea, Ghana (Kintampo).

Asia

Combodia (Pursat), Combodia (Pailin), Thailand (Sisakhet);
Vietnam, Laos, Combodia (Ratanakiri), Combodia (Preah Vihear);
Bangladesh, Myanmar, Thailand (Mae Sot), Thailand (Ranong);

create basic shiny app interface

Move plotting functions to deploid-r

r scripts

https://github.com/mcveanlab/DEploid/blob/master/utilities/dEploidTools.r

https://github.com/mcveanlab/DEploid-r

devtools cheasheet

https://www.rstudio.com/wp-content/uploads/2015/06/devtools-cheatsheet.pdf

requirements

shiny
plotly
dygraphs
leaflet
shinythemes
quantmod
RCurl

2017727_939_server.R is a tmp file, to be removed

circle wsaf

https://github.com/mcveanlab/DEploid/blob/master/utilities/dEploidTools.r#L403

Use for loop to rewrite proportions plot

Sequence data exploration

Similar to deploid stuff, four figures. With some explanation

tidy up files

create a remove dir, move DEploid existing functions to the dir

selectInput "Where is it coming from" disappears

The selectInput "Where is it coming from" disappears when the WSAF vs POS plot (the one using dygraph) is added

read vcf paper, what is vcf

https://en.wikipedia.org/wiki/Variant_Call_Format

put lats and longs into a file

country, lats, longs

use amazon to host DEploid-ShinyApp

http://www.exegetic.biz/blog/2015/05/hosting-shiny-on-amazon-ec2/

coverageGlobal is not found when App is ran for the first time

Contact Oxford it for publication

instructions and notes on the first page

clusterNames.1 = c("Thailand")
clusterNames.2 = c("Indonesia", "Malaysia", "Papua New Guinea")
clusterNames.3 = c("Cambodia", "Vietnam", "Laos")
clusterNames.4 = c("Myanmar (Burma)", "China", "Madagascar", "Sri Lanka", "Brazil", "India")

plot histogram of wsaf

total coverage, allele count

https://github.com/mcveanlab/DEploid/blob/master/utilities/dEploidTools.r#L275

snap shot of the program on github readme page

r shiny cheatsheet

https://www.rstudio.com/wp-content/uploads/2016/01/shiny-cheatsheet.pdf

upload vcf and plot ref vs alt

chrom sizes

CHROM CHROMSIZE
Pf3D7_01_v3 643292
Pf3D7_02_v3 947102
Pf3D7_03_v3 1060087
Pf3D7_04_v3 1204112
Pf3D7_05_v3 1343552
Pf3D7_06_v3 1418244
Pf3D7_07_v3 1501717
Pf3D7_08_v3 1419563
Pf3D7_09_v3 1541723
Pf3D7_10_v3 1687655
Pf3D7_11_v3 2038337
Pf3D7_12_v3 2271478
Pf3D7_13_v3 2895605
Pf3D7_14_v3 3291871

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