R/sample-module.R
In fbreitwieser/pavian: Visualize and analyze metagenomics classification results
Defines functions
sampleModule
sampleModuleUI_function
sampleModuleUI
figure_options
Documented in
sampleModule
sampleModuleUI
library(shiny)
library(shinydashboard)
library(shinyjs)
library(magrittr)
## TODOL Make Sankey work for '-' taxRanks
tax_taxRanks <- c("D","K","P","C","O","F","G","S")
tax_taxRank_names <- c("D"="Domain","K"="Kingdom","P"="Phylum","C"="Clade","O"="Order","F"="Family","G"="Genus","S"="Species", "-"="-", "T"="Strain")
figure_options <- function(ns) {
shiny::tagList(checkboxGroupInput(ns("taxRanks"),"Taxonomical ranks to display",tax_taxRanks,setdiff(tax_taxRanks,c("O","C","-")), inline = TRUE),
sliderInput(ns("sankey_maxn"), "Number of taxa at each level", 1, 25, value = 10, step = 1),
sliderInput(ns("scalingFactor"),"Scale distance between nodes", value = .9, min = .5, max = 1.5, step=.05),
sliderInput(ns("height"),"Figure height", value = 400, min = 300, max = 1200, step=50),
sliderInput(ns("nodeStrokeWidth"),"Node border width", value = 0, min = 0, max = 5, step=1),
sliderInput(ns("linkOpacity"),"Opacity of links", value = .6, min = .1, max = 1, step=.1),
sliderInput(ns("textXPos"),"Node label margins", value = 1, min = 0, max = 5, step=.5),
checkboxInput(ns("show_numbers"),"Show numbers above nodes", value = TRUE),
checkboxInput(ns("color_links"),"Color the flow", value = TRUE),
shinyjs::hidden(sliderInput(ns("curvature"),"Curvature", value = .5, min = 0, max = 1, step=.01)),
shinyjs::hidden(radioButtons(ns("linkType"), "linkType", selected = "path2", choices = c("bezier", "l-bezier", "trapez", "path1","path2"), inline = TRUE)))
}
#' UI part for sample module
#'
#' @param id Shiny namespace id
#'
#' @return UI elements for sample module
#' @export
#' @import shiny
sampleModuleUI <- function(id) {
ns <- shiny::NS(id)
uiOutput(ns("UI"))
}
sampleModuleUI_function <- function(ns, samples, selected_sample = NULL) {
if (!is.null(selected_sample) && is.null(selected_sample)) {
selected_sample = selected_sample()
} else {
selected_sample = samples[1]
}
shiny::tagList(
fluidRow(
div(class="col-lg-5 col-md-6 col-sm-6 col-xs-12",
div(class="col-lg-4 col-md-5 col-sm-12 lessPadding", style="font-size: 18px;", HTML("<label>Select sample<label>")),
div(class="col-lg-8 col-md-7 col-sm-12 lessPadding", style="font-size: 18px;",
selectInput(
ns('sample_selector'), label = NULL,
choices = samples, selected = selected_sample,
multiple = getOption("pavian.devel", FALSE), selectize = TRUE,
width = '100%'
))),
div(class="col-lg-7 col-md-6 col-sm-6 col-xs-12",
div(class="col-lg-2 col-md-4 col-sm-12 lessPadding", HTML("<label>Filter taxa</label>")),
div(class="col-lg-10 col-md-8 col-sm-12 lessPadding",
selectizeInput(
ns('contaminant_selector'), label = NULL,
allcontaminants, selected = c("artificial sequences", "Chordata", "unclassified"),
multiple = TRUE, options = list(maxItems = 25, create = TRUE, placeholder = 'Filter clade'),
width = "100%"
)
)
)
),
fluidRow(
div(class = "col-lg-8 col-md-12", style = "padding: 0px",
tabBox(width=12,
tabPanel("Sankey visualization",
div(style="display:inline-block", "Hover over a node to see the abundance of the taxon in other samples."),
div(style="display:inline-block", shinyWidgets::dropdownButton(figure_options(ns), circle = FALSE, label = "Configure Sankey ...")),
div(uiOutput(ns("dynamic_sankey")), style="border: 1px solid lightgray"),
br(),
downloadLink(ns("save_sankey"),"Save Network")
),
#tabPanel("Partition visualization",
# selectInput(ns("d3part_charttype"),
# label = "Chart type", choices = c('sunburst','treemap','circle_treemap','partition_chart','icicle'), selected="sunburst"),
# D3partitionR::D3partitionROutput(ns("D3partionR"))
# ),
tabPanel("Table",
"Click a row to see the abundance of the taxon in other samples.",
div(style = 'overflow-x: scroll', DT::dataTableOutput(ns('dt_sample_view'))),
br(),
downloadButton(ns('downloadData'), 'Download full table in tab-separated value format')),
tabPanel("Text",
shinyjs::hidden(sliderInput(ns("quantile"),"Amount of data to show", value = 100, min = 1, max = 100, step = 1)),
numericInput(ns("min_reads"),"Minimum number of reads", value = 1, step = 1),
htmlOutput(ns('text')))
)),
div(class = "col-lg-4 col-md-12", style = "padding: 0px",
tabBox(width=12, id = ns("across_sample_tabbox"),
tabPanel("Across samples", status = "success",
uiOutput(ns("sankey_hover_plots")))
)
),
box(width=12,uiOutput(ns("selected_lineage")))
)
)
}
#' Server part for sample module
#'
#' @param input Shiny input object.
#' @param output Shiny output object.
#' @param session Shiny session object.
#' @param sample_data Samples \code{data.frame}.
#' @param reports List of reports.
#' @param tax_data Taxonomy data.
#' @param clade_reads Clade reads.
#' @param taxon_reads Taxon reads.
#' @param selected_sample Pre-selected sample.
#' @param datatable_opts Additional datatable opts (mostly $class).
#'
#' @return Sample module server functionality
#' @export
sampleModule <- function(input, output, session, sample_data, reports,
tax_data, clade_reads, taxon_reads,
selected_sample = NULL, datatable_opts = NULL) {
output$UI <- renderUI({
req(reports())
sampleModuleUI_function(session$ns, names(reports()), selected_sample)
})
sankey_opts_state <- reactiveValues(visible = TRUE)
hover_plots <- reactiveValues(taxon = NULL, report = 1)
observeEvent(input$sankey_opts, {
sankey_opts_state$visible <- !sankey_opts_state$visible
toggle_elems <- c("ext_sankey_opts")
if (sankey_opts_state$visible) {
lapply(toggle_elems, shinyjs::show)
updateActionButton(session, "sankey_opts", label = "Hide options")
} else {
lapply(toggle_elems, shinyjs::hide)
updateActionButton(session, "sankey_opts", label = "Show options")
}
})
#observe({
#shinyjs::show("iterations")
# ss <- 1
# if (!is.null(selected_sample) && !is.null(selected_sample())){
# ss <- selected_sample()
# }
# updateSelectInput(session, 'sample_selector',
# choices = names(reports()),
# selected = names(reports())[ss])
#})
#observeEvent(reports(), {
# updateSelectInput(session, 'sample_selector',
# choices = names(reports()),
# selected = names(reports())[1])
#})
#observeEvent(selected_sample, {
# validate(need(selected_sample <= length(reports()), message = "Selected sample number too high."))
# updateSelectInput(session, 'sample_selector',
# choices = names(reports()),
# selected = names(reports())[selected_sample])
#})
sample_view_report <- reactive({
validate(need(input$sample_selector,message="Select sample sets with reports"))
my_report <- reports()[[input$sample_selector[1]]]
validate(need(my_report, "No sample with that name"))
## filter contaminants
for (c in input$contaminant_selector)
my_report <- filter_taxon(my_report, c)
my_report
})
sample_view_reports <- reactive ({
validate(need(input$sample_selector,message="Select sample sets with reports"))
lapply(input$sample_selector, function(i) {
my_report <- reports()[[i]]
validate(need(my_report, "No sample with that name"))
## filter contaminants
for (c in input$contaminant_selector)
my_report <- filter_taxon(my_report, c)
my_report
})
})
#############################################################################
## Sample viewer outputs
output$selected_lineage <- renderUI({
req(hover_plots$taxon)
my_report <- sample_view_reports()[[hover_plots$report]]
my_report$name <- sub("^._","",my_report$name)
sel_row <- my_report[which(my_report$name == hover_plots$taxon)[1], , drop=FALSE]
shiny::tagList(
HTML("Selected taxon lineage: "),
HTML(beautify_taxLineage(sel_row$taxLineage, remove_last=FALSE, break_it_up=TRUE)),
p(HTML(paste0("Rank ", strong(tax_taxRank_names[sel_row$taxRank]),
{if ("taxID" %in% colnames(sel_row)) {
HTML(paste0(", TaxID ", sel_row$taxID, " [",
a(href=sprintf("https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=%s", sel_row$taxID), target="_blank", "NCBI Taxonomy"), ", ",
a(href=sprintf("https://www.ncbi.nlm.nih.gov/assembly/?term=txid%s[Organism:exp]", sel_row$taxID), target="_blank", "Assemblies"),", "))
} else { HTML("[")}},"",
a(href=sprintf("https://www.ncbi.nlm.nih.gov/pubmed/?term=%s", sel_row$name), target="_blank", "PubMed"),", ",
a(href=sprintf("https://scholar.google.at/scholar?q=%s", sel_row$name), target="_blank"), "Google Scholar"),"]"))
)
})
output$dynamic_sankey <- renderUI({
ns <- session$ns
#sankeyD3::sankeyNetworkOutput(ns("sankey"), width = "100%",
# height = paste0(ifelse(is.null(input$height), 500, input$height),"px"))
do.call(shiny::tagList,
lapply(seq_along(input$sample_selector), function(i) {
sankeyD3::sankeyNetworkOutput(ns(paste0("sankey",i)), width = "100%",
height = paste0(ifelse(is.null(input$height), 500, input$height),"px"))
}))
})
output$sankey_hover_plots <- renderUI({
validate(need(length(reports()) > 1, message="Need more than one sample in sample set."))
validate(need(hover_plots$taxon, message="Hover or select a taxon to display reads across samples."))
ns <- session$ns
my_report <- sample_view_report()
my_report$name <- sub("^._","",my_report$name)
sel_row <- my_report[which(my_report$name == hover_plots$taxon)[1], , drop=FALSE]
req(sel_row)
shinyjs::runjs(sprintf("$('ul#sample-across_sample_tabbox>li>a').text('%s across samples')", hover_plots$taxon))
shiny::tagList(
"Number of reads across all samples ","(",downloadLink(ns("save_plot1"),"PDF"),")",
plotOutput(ns("plot1"), height=paste0(max(200,input$height/1.5-75),"px"), click = ns("plot_click")),
#"Percent of reads (after filtering) (",downloadLink(ns("save_plot2"),"PDF"),")",
#plotOutput(ns("plot2"), height=paste0(max(200,input$height/2-75),"px"), click = ns("plot_click")),
"Legend: The turqoise bar shows the number of reads that are identified at the specific taxon; the orange bar shows the number of reads identified at children of the specified taxon.",
conditionalPanel("typeof input.sankey_hover != 'undefined'", actionLink(ns("show_in_comparison"),"Show in comparison table"))
)
})
plot_it <- function(normalize = FALSE) {
requireNamespace("ggplot2")
#requireNamespace("cowplot")
req(hover_plots$taxon)
selected_taxon <- hover_plots$taxon
taxIndex <- which(tax_data()$name == selected_taxon)[1]
clade_reads_m <- na0(clade_reads()[taxIndex, ]) - na0(taxon_reads()[taxIndex,])
short_name <- substr(sample_data()$Name, 1, 10)
for (si in unique(short_name)) {
sel <- si %in% short_name
if (sum(sel) > 1) {
short_name[sel] <- sprintf("%s-%s", short_name[sel], seq_len(sum(sel)))
}
}
if (any(duplicated(short_name))) {
short_name[duplicated(short_name)]
}
mydf <- data.frame(sample=rep(factor(short_name, levels=short_name),2),
type=factor(rep(c("in total", "at taxon"), each=ncol(clade_reads())), levels = c("in total", "at taxon")),
reads=c(clade_reads_m, taxon_reads()[taxIndex,]),
pos=c(clade_reads()[taxIndex,], taxon_reads()[taxIndex,]))
colvec <- ifelse(colnames(clade_reads()) %in% input$sample_selector, "red","black")
#if (normalize) {
# mydf$reads <- 100*mydf$reads / rep(sum_clade_reads(), each = 2)
#}
## TODO: Replace by D3 graph?
## See e.g. http://eyeseast.github.io/visible-data/2013/08/28/responsive-charts-with-d3/
ggplot(mydf, aes(x=sample)) +
geom_bar(aes(y=reads, fill=type), stat="identity", position="stack") +
xlab("") + ylab("") +
scale_y_continuous(limits=c(0,max(mydf$pos, na.rm=T)*1.1), expand=c(0,0)) +
scale_fill_manual("", values = c("in total"="#fc8d62", "at taxon"="#66c2a5")) +
my_gg_theme(12) +
theme(
axis.ticks = element_blank(),
axis.text.x = element_text(colour=colvec, angle=90, vjust=1,hjust=1, size = 10),
legend.position = "none"
)
}
output$save_plot1 <- downloadHandler(
filename = function() {
paste("plot1-", Sys.Date(), ".pdf", sep="")
},
content = function(file) {
ggsave(file, plot_it(FALSE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1))
}
)
output$plot1 <- renderPlot({
plot_it(FALSE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1)
}, bg="transparent")
output$save_plot2 <- downloadHandler(
filename = function() {
paste("plot2-", Sys.Date(), ".pdf", sep="")
},
content = function(file) {
ggsave(file, plot_it(TRUE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1))
}
)
output$plot2 <- renderPlot({
plot_it(TRUE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1)
}, bg="transparent")
observeEvent(input$plot_click, {
if (round(input$plot_click$x) %in% seq_along(names(reports())))
updateSelectizeInput(session, "sample_selector", selected = names(reports())[round(input$plot_click$x)])
})
output$sankey <- sankeyD3::renderSankeyNetwork({ sankey_network() })
output$sankey1 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[1]] })
output$sankey2 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[2]] })
output$sankey3 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[3]] })
output$sankey4 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[4]] })
output$sankey5 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[5]] })
output$sankey6 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[6]] })
output$sankey7 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[7]] })
output$sankey8 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[8]] })
output$sankey9 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[9]] })
output$sankey10 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[10]] })
observeEvent(input$sankey_hover, { hover_plots$taxon <- input$sankey_hover })
observeEvent(input$sankey1_hover, { hover_plots$taxon <- input$sankey1_hover; hover_plots$report <- 1; })
observeEvent(input$sankey2_hover, { hover_plots$taxon <- input$sankey2_hover; hover_plots$report <- 2; })
observeEvent(input$sankey3_hover, { hover_plots$taxon <- input$sankey3_hover; hover_plots$report <- 3; })
observeEvent(input$sankey4_hover, { hover_plots$taxon <- input$sankey4_hover; hover_plots$report <- 4; })
observeEvent(input$sankey5_hover, { hover_plots$taxon <- input$sankey5_hover; hover_plots$report <- 5; })
observeEvent(input$sankey6_hover, { hover_plots$taxon <- input$sankey6_hover; hover_plots$report <- 6; })
observeEvent(input$sankey7_hover, { hover_plots$taxon <- input$sankey7_hover; hover_plots$report <- 7; })
observeEvent(input$sankey8_hover, { hover_plots$taxon <- input$sankey8_hover; hover_plots$report <- 8; })
observeEvent(input$sankey9_hover, { hover_plots$taxon <- input$sankey9_hover; hover_plots$report <- 9; })
observeEvent(input$sankey10_hover, { hover_plots$taxon <- input$sankey10_hover; hover_plots$report <- 10; })
observeEvent(input$dt_sample_view_rows_selected, {
hover_plots$taxon <- sub("^._", "", sample_view_report()[input$dt_sample_view_rows_selected,"name"])
})
observeEvent(input$sankey_hover, {
req(dt_sample_view_proxy)
DT::updateSearch(dt_sample_view_proxy, list(global=input$sankey_hover))
DT::updateSearch(dt_sample_view_proxy1, list(global=input$sankey_hover))
})
tbx <- reactive({
dat <- sample_data()
if (!"CentrifugeOutFilePath" %in% colnames(dat))
return()
cf_out <- dat[dat$Name == input$sample_selector[1],"CentrifugeOutFilePath"]
if (!file.exists(cf_out) || !file.exists(paste0(cf_out,".tbi")))
return()
req(requireNamespace("Rsamtools"))
return(Rsamtools::TabixFile(cf_out, yieldSize = 100))
})
tbx_results <- reactive({
req(tbx)
req(sample_view_report())
req(input$dt_sample_view_rows_selected)
#scanTabix(tbx(),
# GRanges(sample_view_report()[input$dt_sample_view_rows_selected, "taxID"], IRanges(c(50), width=100000)))[[1]]
})
tbx_results_df <- reactive({
req(tbx_results())
#read.delim(tbx_results(), header=F,
# col.names = c("readID","seqID","taxID","score","2ndBestScore","hitLength","queryLength","numMatches","readSeq"))
})
output$txt_selected_name <- renderText({
input$sankey_clicked
})
all_names <- reactive ({
sub("^._","", sort(unique(unlist(sapply(reports(), function(x) x$name[x$taxRank != "-"])))))
})
colourScale <- reactive({
colourScale <- sankeyD3::JS(sprintf("d3.scaleOrdinal().range(d3.schemeCategory20b).domain([%s])",
paste0('"',c(all_names(),"other"),'"',collapse=",")))
})
output$save_sankey <- downloadHandler(filename = function() { paste0("sankey-",input$sample_selector[1],".html") },
content = function(con) {
a <- sankey_networks()[[1]]
a$sizingPolicy$defaultHeight <- 1080
a$sizingPolicy$defaultWidth <- 1920
htmlwidgets::saveWidget(a, file=con)
})
sankey_network <- reactive( {
my_report <- sample_view_report()
req(my_report)
# filter report with rows as selected in the table
if (isTRUE(input$synchronize_table) &&
length(input$dt_sample_view_rows_all) > 0)
my_report <- my_report[sort(input$dt_sample_view_rows_all), ]
#my_report$name <- sub("._", "", my_report$name)
#my_report <- my_report[, c("depth", "cladeReads", "name")]
#my_report$name <- sub("^._","",my_report$name)
#eng <- get_nodes_and_links(my_report, 10)
validate(need(any(input$taxRanks %in% my_report$taxRank), message = "Report does not have required taxonomy ranks"))
build_sankey_network(my_report, taxRanks=input$taxRanks, maxn=input$sankey_maxn,
# Sankey options
xScalingFactor = input$scalingFactor,
nodePadding = ifelse(input$show_numbers, 13, 8),
nodeStrokeWidth = input$nodeStrokeWidth,
showNodeValues = input$show_numbers,
linkOpacity = input$linkOpacity,
linkType = input$linkType,
nodeLabelMargin = input$textXPos,
height = input$height,
curvature = input$curvature,
colourScale = colourScale(),
LinkGroup = ifelse(input$color_links, "source_name", NA)
) %>% shinyTryCatch(message="building Sankey network")
})
sankey_networks <- reactive({
lapply(seq_along(input$sample_selector), function(i) {
my_report <- sample_view_reports()[[i]]
req(my_report)
# filter report with rows as selected in the table
if (isTRUE(input$synchronize_table) &&
length(input$dt_sample_view_rows_all) > 0)
my_report <- my_report[sort(input$dt_sample_view_rows_all), ]
#my_report$name <- sub("._", "", my_report$name)
#my_report <- my_report[, c("depth", "cladeReads", "name")]
#my_report$name <- sub("^._","",my_report$name)
#eng <- get_nodes_and_links(my_report, 10)
validate(need(any(input$taxRanks %in% my_report$taxRank), message = "Report does not have required taxonomy ranks"))
build_sankey_network(my_report, taxRanks=input$taxRanks, maxn=input$sankey_maxn,
#title = input$sample_selector[i],
# Sankey options
xScalingFactor = input$scalingFactor,
nodePadding = ifelse(input$show_numbers, 13, 8),
nodeStrokeWidth = input$nodeStrokeWidth,
showNodeValues = input$show_numbers,
linkOpacity = input$linkOpacity,
linkType = input$linkType,
nodeLabelMargin = input$textXPos,
height = input$height,
curvature = input$curvature,
colourScale = colourScale(),
LinkGroup = ifelse(input$color_links, "source_name", NA)
) %>% shinyTryCatch(message="building Sankey network")
})
})
output$text <- renderUI({
my_report <- sample_view_report()
name_format <- function(node_name) {
paste(sprintf("<a href='#' onclick=\"Shiny.onInputChange('%s','%s');\" class='name-link'><nobr>%s</nobr></a>",
session$ns("sankey_hover"),node_name, node_name), collapse = "<wbr>>")
}
# HTML(
quant1 <- stats::quantile(my_report$cladeReads[my_report$taxonReads > 0], probs=1-input$quantile/100)
div(style="line-height: 1;",
text_representation(my_report,
name_format = name_format,
reads_format = function(x, color) sprintf("<span style='background-color:%s;'>%s</span>", color, x),
min_reads = input$min_reads, collapse = "<br/>\n")
)
# )
})
dt_sample_view_proxy <- DT::dataTableProxy('dt_sample_view')
dt_sample_view_proxy1 <- DT::dataTableProxy(session$ns('dt_sample_view'))
output$dt_sample_view <- DT::renderDataTable({
my_report <- sample_view_report()
my_report$taxLineage <- beautify_taxLineage(my_report$taxLineage, TRUE)
my_report$taxRank <- as.factor(my_report$taxRank)
#my_report$Percent <-
# 100 * signif(my_report$cladeReads / sum(my_report$taxonReads, na.rm = TRUE), 3)
my_report$coverage <- NULL
my_report$taxRankperc <- NULL
my_report$percentage <- signif(100*my_report$cladeReads/max(my_report$cladeReads),4)
my_report$depth <- NULL
my_report$name <- my_report$name %>% sub("^._", "", .) %>% gsub(" ", " ", .)
#my_report <- my_report[my_report$taxonReads > 0, ]
colnames(my_report) <- beautify_string(colnames(my_report))
if (!max(my_report$CladeReads) > 1000) {
my_report[,c("CladeReads", "TaxonReads")] <- signif(my_report[,c("CladeReads", "TaxonReads")], digits = 4)
}
dt <- DT::datatable(my_report,
filter = 'bottom', selection = 'single',
class = datatable_opts$class,
extensions = datatable_opts$extensions,
escape = FALSE, rownames = FALSE,
options = list(buttons = common_buttons(input$sample_selector[1], "results"),
columnDefs=list(list(targets = seq(from=, to=2), visible=TRUE, orderSequence = c('desc','asc'))))
)
if (max(my_report$CladeReads) > 1000) {
dt <- dt %>% DT::formatCurrency(c("CladeReads", "TaxonReads"), digits = 0, currency = "")
}
dt %>%
DT::formatStyle(c("CladeReads","TaxonReads"),
background = styleColorBar2(c(0,my_report$CladeReads,na.rm=T), 'lightblue')) %>%
DT::formatString(c("Percentage"), suffix = '%') %>%
DT::formatStyle(c("Percentage"),
background = styleColorBar2(c(0,100,na.rm=T), 'lightblue'))
}, server = TRUE)
output$downloadData <- downloadHandler(
filename = function() { sprintf("%s-report-%s.tsv", input$sample_selector[1], format(Sys.time(), "%y%m%d")) },
content = function(file) {
utils::write.table(beautify_colnames(sample_view_report()), file, row.names = FALSE, sep = "\t")
}
)
## When a row (i.e. a taxonomical entry) gets selected in the sample view table, an action button appears to view the species in the overview
output$view_in_samples_comparison <- renderUI({
req(input$dt_sample_view_rows_selected)
selected_row <- input$dt_sample_view_rows_selected
my_report <- sample_view_report()
selected_sample <-
my_report[input$dt_sample_view_rows_selected, "name"]
selected_sample <- sub("^u_", "", selected_sample)
selected_sample <- sub("^-_", "", selected_sample)
selected_sample <- sub("^d_", "domain ", selected_sample)
selected_sample <- sub("^k_", "kingdom ", selected_sample)
selected_sample <- sub("^p_", "phylum ", selected_sample)
selected_sample <- sub("^o_", "order ", selected_sample)
selected_sample <- sub("^f_", "family ", selected_sample)
selected_sample <- sub("^g_", "genus ", selected_sample)
selected_sample <- sub("^s_", "species ", selected_sample)
## TODO: Add a custom search functionality
#actionButton("view_selected_in_samples_comparison",paste("--> View abundances of ",selected_sample,"across samples"))
})
output$blastn <- renderUI({
req(tbx_results_df())
#str(tbx_results_df())
## TODO: Add a custom search functionality
#actionButton("view_selected_in_samples_comparison",paste("--> View abundances of ",selected_sample,"across samples"))
})
observeEvent(input$view_selected_in_samples_comparison, {
my_report <- sample_view_report()
selected_sample <-
my_report[input$dt_sample_view_rows_selected, "name"]
updateTabsetPanel(session, "main_page", selected = "Sample comparison")
}, ignoreNULL = TRUE)
## D3partitionR does not display - might be added back at a later point in time
# output$D3partionR <- D3partitionR::renderD3partitionR({
# library(D3partitionR)
# my_report <- sample_view_report()
# my_report <- my_report[my_report$cladeReads > 0 & my_report$taxonReads > 10 & grepl("^._root",my_report$taxLineage), ]
# #taxLineage <- sub("^._root.","",my_report$taxLineage) %>% gsub("._","", .)
# strsplit(my_report$taxLineage, "|", fixed=T) %>% lapply(grep, pattern= "^-_", invert = T, value = T)
#
# domains <- c("d", "p", "c", "f", "g", "s")
# pattern <- sprintf("^[%s]_", paste(domains, collapse=""))
# res <- strsplit(my_report$taxLineage, "|", fixed=T) %>%
# lapply(function(x) {
# y <- grep(pattern, x, value = T)
# d <- sub("_.*", "", y)
# n <- sub("^._", "", y)
# names(n) <- d
# #xx <- n[domains]
# #xx[is.na(xx)] <- "NA"
# #xx
# n[domains]
# }) %>% do.call(rbind, .)
# colnames(res) <- domains
# res <- data.frame(res, stringsAsFactors = FALSE)
# sel <- !apply(is.na(res), 1, any) & my_report$taxonReads > 0
# #sel <- !apply(is.na(res), 1, all)
# #sel <- my_report$cladeReads
# res$N <- my_report$taxonRead
# res <- res[sel, ]
# library(plyr)
# res <- ddply(res, domains, function(x) {
# a = x[1, , drop=F]
# a$N = sum(x$N)
# a
# } )
#
# D3partitionR::D3partitionR() %>%
# D3partitionR::add_data(res, count = 'N', steps = domains, color='N') %>%
# #D3partitionR::add_title(list(text=input$sample_selector)) %>%
# set_chart_type(input$d3part_charttype) %>%
# plot
# })
#reactive({
# req(input$show_in_comparison)
# return(isolate(hover_plots$taxon));
#})
}
fbreitwieser/pavian documentation built on Jan. 5, 2024, 1:43 a.m.
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Defines functions sampleModule sampleModuleUI_function sampleModuleUI figure_options
Documented in sampleModule sampleModuleUI
library(shiny)
library(shinydashboard)
library(shinyjs)
library(magrittr)
## TODOL Make Sankey work for '-' taxRanks
tax_taxRanks <- c("D","K","P","C","O","F","G","S")
tax_taxRank_names <- c("D"="Domain","K"="Kingdom","P"="Phylum","C"="Clade","O"="Order","F"="Family","G"="Genus","S"="Species", "-"="-", "T"="Strain")
figure_options <- function(ns) {
shiny::tagList(checkboxGroupInput(ns("taxRanks"),"Taxonomical ranks to display",tax_taxRanks,setdiff(tax_taxRanks,c("O","C","-")), inline = TRUE),
sliderInput(ns("sankey_maxn"), "Number of taxa at each level", 1, 25, value = 10, step = 1),
sliderInput(ns("scalingFactor"),"Scale distance between nodes", value = .9, min = .5, max = 1.5, step=.05),
sliderInput(ns("height"),"Figure height", value = 400, min = 300, max = 1200, step=50),
sliderInput(ns("nodeStrokeWidth"),"Node border width", value = 0, min = 0, max = 5, step=1),
sliderInput(ns("linkOpacity"),"Opacity of links", value = .6, min = .1, max = 1, step=.1),
sliderInput(ns("textXPos"),"Node label margins", value = 1, min = 0, max = 5, step=.5),
checkboxInput(ns("show_numbers"),"Show numbers above nodes", value = TRUE),
checkboxInput(ns("color_links"),"Color the flow", value = TRUE),
shinyjs::hidden(sliderInput(ns("curvature"),"Curvature", value = .5, min = 0, max = 1, step=.01)),
shinyjs::hidden(radioButtons(ns("linkType"), "linkType", selected = "path2", choices = c("bezier", "l-bezier", "trapez", "path1","path2"), inline = TRUE)))
}
#' UI part for sample module
#'
#' @param id Shiny namespace id
#'
#' @return UI elements for sample module
#' @export
#' @import shiny
sampleModuleUI <- function(id) {
ns <- shiny::NS(id)
uiOutput(ns("UI"))
}
sampleModuleUI_function <- function(ns, samples, selected_sample = NULL) {
if (!is.null(selected_sample) && is.null(selected_sample)) {
selected_sample = selected_sample()
} else {
selected_sample = samples[1]
}
shiny::tagList(
fluidRow(
div(class="col-lg-5 col-md-6 col-sm-6 col-xs-12",
div(class="col-lg-4 col-md-5 col-sm-12 lessPadding", style="font-size: 18px;", HTML("<label>Select sample<label>")),
div(class="col-lg-8 col-md-7 col-sm-12 lessPadding", style="font-size: 18px;",
selectInput(
ns('sample_selector'), label = NULL,
choices = samples, selected = selected_sample,
multiple = getOption("pavian.devel", FALSE), selectize = TRUE,
width = '100%'
))),
div(class="col-lg-7 col-md-6 col-sm-6 col-xs-12",
div(class="col-lg-2 col-md-4 col-sm-12 lessPadding", HTML("<label>Filter taxa</label>")),
div(class="col-lg-10 col-md-8 col-sm-12 lessPadding",
selectizeInput(
ns('contaminant_selector'), label = NULL,
allcontaminants, selected = c("artificial sequences", "Chordata", "unclassified"),
multiple = TRUE, options = list(maxItems = 25, create = TRUE, placeholder = 'Filter clade'),
width = "100%"
)
)
)
),
fluidRow(
div(class = "col-lg-8 col-md-12", style = "padding: 0px",
tabBox(width=12,
tabPanel("Sankey visualization",
div(style="display:inline-block", "Hover over a node to see the abundance of the taxon in other samples."),
div(style="display:inline-block", shinyWidgets::dropdownButton(figure_options(ns), circle = FALSE, label = "Configure Sankey ...")),
div(uiOutput(ns("dynamic_sankey")), style="border: 1px solid lightgray"),
br(),
downloadLink(ns("save_sankey"),"Save Network")
),
#tabPanel("Partition visualization",
# selectInput(ns("d3part_charttype"),
# label = "Chart type", choices = c('sunburst','treemap','circle_treemap','partition_chart','icicle'), selected="sunburst"),
# D3partitionR::D3partitionROutput(ns("D3partionR"))
# ),
tabPanel("Table",
"Click a row to see the abundance of the taxon in other samples.",
div(style = 'overflow-x: scroll', DT::dataTableOutput(ns('dt_sample_view'))),
br(),
downloadButton(ns('downloadData'), 'Download full table in tab-separated value format')),
tabPanel("Text",
shinyjs::hidden(sliderInput(ns("quantile"),"Amount of data to show", value = 100, min = 1, max = 100, step = 1)),
numericInput(ns("min_reads"),"Minimum number of reads", value = 1, step = 1),
htmlOutput(ns('text')))
)),
div(class = "col-lg-4 col-md-12", style = "padding: 0px",
tabBox(width=12, id = ns("across_sample_tabbox"),
tabPanel("Across samples", status = "success",
uiOutput(ns("sankey_hover_plots")))
)
),
box(width=12,uiOutput(ns("selected_lineage")))
)
)
}
#' Server part for sample module
#'
#' @param input Shiny input object.
#' @param output Shiny output object.
#' @param session Shiny session object.
#' @param sample_data Samples \code{data.frame}.
#' @param reports List of reports.
#' @param tax_data Taxonomy data.
#' @param clade_reads Clade reads.
#' @param taxon_reads Taxon reads.
#' @param selected_sample Pre-selected sample.
#' @param datatable_opts Additional datatable opts (mostly $class).
#'
#' @return Sample module server functionality
#' @export
sampleModule <- function(input, output, session, sample_data, reports,
tax_data, clade_reads, taxon_reads,
selected_sample = NULL, datatable_opts = NULL) {
output$UI <- renderUI({
req(reports())
sampleModuleUI_function(session$ns, names(reports()), selected_sample)
})
sankey_opts_state <- reactiveValues(visible = TRUE)
hover_plots <- reactiveValues(taxon = NULL, report = 1)
observeEvent(input$sankey_opts, {
sankey_opts_state$visible <- !sankey_opts_state$visible
toggle_elems <- c("ext_sankey_opts")
if (sankey_opts_state$visible) {
lapply(toggle_elems, shinyjs::show)
updateActionButton(session, "sankey_opts", label = "Hide options")
} else {
lapply(toggle_elems, shinyjs::hide)
updateActionButton(session, "sankey_opts", label = "Show options")
}
})
#observe({
#shinyjs::show("iterations")
# ss <- 1
# if (!is.null(selected_sample) && !is.null(selected_sample())){
# ss <- selected_sample()
# }
# updateSelectInput(session, 'sample_selector',
# choices = names(reports()),
# selected = names(reports())[ss])
#})
#observeEvent(reports(), {
# updateSelectInput(session, 'sample_selector',
# choices = names(reports()),
# selected = names(reports())[1])
#})
#observeEvent(selected_sample, {
# validate(need(selected_sample <= length(reports()), message = "Selected sample number too high."))
# updateSelectInput(session, 'sample_selector',
# choices = names(reports()),
# selected = names(reports())[selected_sample])
#})
sample_view_report <- reactive({
validate(need(input$sample_selector,message="Select sample sets with reports"))
my_report <- reports()[[input$sample_selector[1]]]
validate(need(my_report, "No sample with that name"))
## filter contaminants
for (c in input$contaminant_selector)
my_report <- filter_taxon(my_report, c)
my_report
})
sample_view_reports <- reactive ({
validate(need(input$sample_selector,message="Select sample sets with reports"))
lapply(input$sample_selector, function(i) {
my_report <- reports()[[i]]
validate(need(my_report, "No sample with that name"))
## filter contaminants
for (c in input$contaminant_selector)
my_report <- filter_taxon(my_report, c)
my_report
})
})
#############################################################################
## Sample viewer outputs
output$selected_lineage <- renderUI({
req(hover_plots$taxon)
my_report <- sample_view_reports()[[hover_plots$report]]
my_report$name <- sub("^._","",my_report$name)
sel_row <- my_report[which(my_report$name == hover_plots$taxon)[1], , drop=FALSE]
shiny::tagList(
HTML("Selected taxon lineage: "),
HTML(beautify_taxLineage(sel_row$taxLineage, remove_last=FALSE, break_it_up=TRUE)),
p(HTML(paste0("Rank ", strong(tax_taxRank_names[sel_row$taxRank]),
{if ("taxID" %in% colnames(sel_row)) {
HTML(paste0(", TaxID ", sel_row$taxID, " [",
a(href=sprintf("https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=%s", sel_row$taxID), target="_blank", "NCBI Taxonomy"), ", ",
a(href=sprintf("https://www.ncbi.nlm.nih.gov/assembly/?term=txid%s[Organism:exp]", sel_row$taxID), target="_blank", "Assemblies"),", "))
} else { HTML("[")}},"",
a(href=sprintf("https://www.ncbi.nlm.nih.gov/pubmed/?term=%s", sel_row$name), target="_blank", "PubMed"),", ",
a(href=sprintf("https://scholar.google.at/scholar?q=%s", sel_row$name), target="_blank"), "Google Scholar"),"]"))
)
})
output$dynamic_sankey <- renderUI({
ns <- session$ns
#sankeyD3::sankeyNetworkOutput(ns("sankey"), width = "100%",
# height = paste0(ifelse(is.null(input$height), 500, input$height),"px"))
do.call(shiny::tagList,
lapply(seq_along(input$sample_selector), function(i) {
sankeyD3::sankeyNetworkOutput(ns(paste0("sankey",i)), width = "100%",
height = paste0(ifelse(is.null(input$height), 500, input$height),"px"))
}))
})
output$sankey_hover_plots <- renderUI({
validate(need(length(reports()) > 1, message="Need more than one sample in sample set."))
validate(need(hover_plots$taxon, message="Hover or select a taxon to display reads across samples."))
ns <- session$ns
my_report <- sample_view_report()
my_report$name <- sub("^._","",my_report$name)
sel_row <- my_report[which(my_report$name == hover_plots$taxon)[1], , drop=FALSE]
req(sel_row)
shinyjs::runjs(sprintf("$('ul#sample-across_sample_tabbox>li>a').text('%s across samples')", hover_plots$taxon))
shiny::tagList(
"Number of reads across all samples ","(",downloadLink(ns("save_plot1"),"PDF"),")",
plotOutput(ns("plot1"), height=paste0(max(200,input$height/1.5-75),"px"), click = ns("plot_click")),
#"Percent of reads (after filtering) (",downloadLink(ns("save_plot2"),"PDF"),")",
#plotOutput(ns("plot2"), height=paste0(max(200,input$height/2-75),"px"), click = ns("plot_click")),
"Legend: The turqoise bar shows the number of reads that are identified at the specific taxon; the orange bar shows the number of reads identified at children of the specified taxon.",
conditionalPanel("typeof input.sankey_hover != 'undefined'", actionLink(ns("show_in_comparison"),"Show in comparison table"))
)
})
plot_it <- function(normalize = FALSE) {
requireNamespace("ggplot2")
#requireNamespace("cowplot")
req(hover_plots$taxon)
selected_taxon <- hover_plots$taxon
taxIndex <- which(tax_data()$name == selected_taxon)[1]
clade_reads_m <- na0(clade_reads()[taxIndex, ]) - na0(taxon_reads()[taxIndex,])
short_name <- substr(sample_data()$Name, 1, 10)
for (si in unique(short_name)) {
sel <- si %in% short_name
if (sum(sel) > 1) {
short_name[sel] <- sprintf("%s-%s", short_name[sel], seq_len(sum(sel)))
}
}
if (any(duplicated(short_name))) {
short_name[duplicated(short_name)]
}
mydf <- data.frame(sample=rep(factor(short_name, levels=short_name),2),
type=factor(rep(c("in total", "at taxon"), each=ncol(clade_reads())), levels = c("in total", "at taxon")),
reads=c(clade_reads_m, taxon_reads()[taxIndex,]),
pos=c(clade_reads()[taxIndex,], taxon_reads()[taxIndex,]))
colvec <- ifelse(colnames(clade_reads()) %in% input$sample_selector, "red","black")
#if (normalize) {
# mydf$reads <- 100*mydf$reads / rep(sum_clade_reads(), each = 2)
#}
## TODO: Replace by D3 graph?
## See e.g. http://eyeseast.github.io/visible-data/2013/08/28/responsive-charts-with-d3/
ggplot(mydf, aes(x=sample)) +
geom_bar(aes(y=reads, fill=type), stat="identity", position="stack") +
xlab("") + ylab("") +
scale_y_continuous(limits=c(0,max(mydf$pos, na.rm=T)*1.1), expand=c(0,0)) +
scale_fill_manual("", values = c("in total"="#fc8d62", "at taxon"="#66c2a5")) +
my_gg_theme(12) +
theme(
axis.ticks = element_blank(),
axis.text.x = element_text(colour=colvec, angle=90, vjust=1,hjust=1, size = 10),
legend.position = "none"
)
}
output$save_plot1 <- downloadHandler(
filename = function() {
paste("plot1-", Sys.Date(), ".pdf", sep="")
},
content = function(file) {
ggsave(file, plot_it(FALSE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1))
}
)
output$plot1 <- renderPlot({
plot_it(FALSE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1)
}, bg="transparent")
output$save_plot2 <- downloadHandler(
filename = function() {
paste("plot2-", Sys.Date(), ".pdf", sep="")
},
content = function(file) {
ggsave(file, plot_it(TRUE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1))
}
)
output$plot2 <- renderPlot({
plot_it(TRUE) +
geom_text(aes(label = f2si2(pos), y=pos), hjust = 0.5, vjust = -.1)
}, bg="transparent")
observeEvent(input$plot_click, {
if (round(input$plot_click$x) %in% seq_along(names(reports())))
updateSelectizeInput(session, "sample_selector", selected = names(reports())[round(input$plot_click$x)])
})
output$sankey <- sankeyD3::renderSankeyNetwork({ sankey_network() })
output$sankey1 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[1]] })
output$sankey2 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[2]] })
output$sankey3 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[3]] })
output$sankey4 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[4]] })
output$sankey5 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[5]] })
output$sankey6 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[6]] })
output$sankey7 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[7]] })
output$sankey8 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[8]] })
output$sankey9 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[9]] })
output$sankey10 <- sankeyD3::renderSankeyNetwork({ sankey_networks()[[10]] })
observeEvent(input$sankey_hover, { hover_plots$taxon <- input$sankey_hover })
observeEvent(input$sankey1_hover, { hover_plots$taxon <- input$sankey1_hover; hover_plots$report <- 1; })
observeEvent(input$sankey2_hover, { hover_plots$taxon <- input$sankey2_hover; hover_plots$report <- 2; })
observeEvent(input$sankey3_hover, { hover_plots$taxon <- input$sankey3_hover; hover_plots$report <- 3; })
observeEvent(input$sankey4_hover, { hover_plots$taxon <- input$sankey4_hover; hover_plots$report <- 4; })
observeEvent(input$sankey5_hover, { hover_plots$taxon <- input$sankey5_hover; hover_plots$report <- 5; })
observeEvent(input$sankey6_hover, { hover_plots$taxon <- input$sankey6_hover; hover_plots$report <- 6; })
observeEvent(input$sankey7_hover, { hover_plots$taxon <- input$sankey7_hover; hover_plots$report <- 7; })
observeEvent(input$sankey8_hover, { hover_plots$taxon <- input$sankey8_hover; hover_plots$report <- 8; })
observeEvent(input$sankey9_hover, { hover_plots$taxon <- input$sankey9_hover; hover_plots$report <- 9; })
observeEvent(input$sankey10_hover, { hover_plots$taxon <- input$sankey10_hover; hover_plots$report <- 10; })
observeEvent(input$dt_sample_view_rows_selected, {
hover_plots$taxon <- sub("^._", "", sample_view_report()[input$dt_sample_view_rows_selected,"name"])
})
observeEvent(input$sankey_hover, {
req(dt_sample_view_proxy)
DT::updateSearch(dt_sample_view_proxy, list(global=input$sankey_hover))
DT::updateSearch(dt_sample_view_proxy1, list(global=input$sankey_hover))
})
tbx <- reactive({
dat <- sample_data()
if (!"CentrifugeOutFilePath" %in% colnames(dat))
return()
cf_out <- dat[dat$Name == input$sample_selector[1],"CentrifugeOutFilePath"]
if (!file.exists(cf_out) || !file.exists(paste0(cf_out,".tbi")))
return()
req(requireNamespace("Rsamtools"))
return(Rsamtools::TabixFile(cf_out, yieldSize = 100))
})
tbx_results <- reactive({
req(tbx)
req(sample_view_report())
req(input$dt_sample_view_rows_selected)
#scanTabix(tbx(),
# GRanges(sample_view_report()[input$dt_sample_view_rows_selected, "taxID"], IRanges(c(50), width=100000)))[[1]]
})
tbx_results_df <- reactive({
req(tbx_results())
#read.delim(tbx_results(), header=F,
# col.names = c("readID","seqID","taxID","score","2ndBestScore","hitLength","queryLength","numMatches","readSeq"))
})
output$txt_selected_name <- renderText({
input$sankey_clicked
})
all_names <- reactive ({
sub("^._","", sort(unique(unlist(sapply(reports(), function(x) x$name[x$taxRank != "-"])))))
})
colourScale <- reactive({
colourScale <- sankeyD3::JS(sprintf("d3.scaleOrdinal().range(d3.schemeCategory20b).domain([%s])",
paste0('"',c(all_names(),"other"),'"',collapse=",")))
})
output$save_sankey <- downloadHandler(filename = function() { paste0("sankey-",input$sample_selector[1],".html") },
content = function(con) {
a <- sankey_networks()[[1]]
a$sizingPolicy$defaultHeight <- 1080
a$sizingPolicy$defaultWidth <- 1920
htmlwidgets::saveWidget(a, file=con)
})
sankey_network <- reactive( {
my_report <- sample_view_report()
req(my_report)
# filter report with rows as selected in the table
if (isTRUE(input$synchronize_table) &&
length(input$dt_sample_view_rows_all) > 0)
my_report <- my_report[sort(input$dt_sample_view_rows_all), ]
#my_report$name <- sub("._", "", my_report$name)
#my_report <- my_report[, c("depth", "cladeReads", "name")]
#my_report$name <- sub("^._","",my_report$name)
#eng <- get_nodes_and_links(my_report, 10)
validate(need(any(input$taxRanks %in% my_report$taxRank), message = "Report does not have required taxonomy ranks"))
build_sankey_network(my_report, taxRanks=input$taxRanks, maxn=input$sankey_maxn,
# Sankey options
xScalingFactor = input$scalingFactor,
nodePadding = ifelse(input$show_numbers, 13, 8),
nodeStrokeWidth = input$nodeStrokeWidth,
showNodeValues = input$show_numbers,
linkOpacity = input$linkOpacity,
linkType = input$linkType,
nodeLabelMargin = input$textXPos,
height = input$height,
curvature = input$curvature,
colourScale = colourScale(),
LinkGroup = ifelse(input$color_links, "source_name", NA)
) %>% shinyTryCatch(message="building Sankey network")
})
sankey_networks <- reactive({
lapply(seq_along(input$sample_selector), function(i) {
my_report <- sample_view_reports()[[i]]
req(my_report)
# filter report with rows as selected in the table
if (isTRUE(input$synchronize_table) &&
length(input$dt_sample_view_rows_all) > 0)
my_report <- my_report[sort(input$dt_sample_view_rows_all), ]
#my_report$name <- sub("._", "", my_report$name)
#my_report <- my_report[, c("depth", "cladeReads", "name")]
#my_report$name <- sub("^._","",my_report$name)
#eng <- get_nodes_and_links(my_report, 10)
validate(need(any(input$taxRanks %in% my_report$taxRank), message = "Report does not have required taxonomy ranks"))
build_sankey_network(my_report, taxRanks=input$taxRanks, maxn=input$sankey_maxn,
#title = input$sample_selector[i],
# Sankey options
xScalingFactor = input$scalingFactor,
nodePadding = ifelse(input$show_numbers, 13, 8),
nodeStrokeWidth = input$nodeStrokeWidth,
showNodeValues = input$show_numbers,
linkOpacity = input$linkOpacity,
linkType = input$linkType,
nodeLabelMargin = input$textXPos,
height = input$height,
curvature = input$curvature,
colourScale = colourScale(),
LinkGroup = ifelse(input$color_links, "source_name", NA)
) %>% shinyTryCatch(message="building Sankey network")
})
})
output$text <- renderUI({
my_report <- sample_view_report()
name_format <- function(node_name) {
paste(sprintf("<a href='#' onclick=\"Shiny.onInputChange('%s','%s');\" class='name-link'><nobr>%s</nobr></a>",
session$ns("sankey_hover"),node_name, node_name), collapse = "<wbr>>")
}
# HTML(
quant1 <- stats::quantile(my_report$cladeReads[my_report$taxonReads > 0], probs=1-input$quantile/100)
div(style="line-height: 1;",
text_representation(my_report,
name_format = name_format,
reads_format = function(x, color) sprintf("<span style='background-color:%s;'>%s</span>", color, x),
min_reads = input$min_reads, collapse = "<br/>\n")
)
# )
})
dt_sample_view_proxy <- DT::dataTableProxy('dt_sample_view')
dt_sample_view_proxy1 <- DT::dataTableProxy(session$ns('dt_sample_view'))
output$dt_sample_view <- DT::renderDataTable({
my_report <- sample_view_report()
my_report$taxLineage <- beautify_taxLineage(my_report$taxLineage, TRUE)
my_report$taxRank <- as.factor(my_report$taxRank)
#my_report$Percent <-
# 100 * signif(my_report$cladeReads / sum(my_report$taxonReads, na.rm = TRUE), 3)
my_report$coverage <- NULL
my_report$taxRankperc <- NULL
my_report$percentage <- signif(100*my_report$cladeReads/max(my_report$cladeReads),4)
my_report$depth <- NULL
my_report$name <- my_report$name %>% sub("^._", "", .) %>% gsub(" ", " ", .)
#my_report <- my_report[my_report$taxonReads > 0, ]
colnames(my_report) <- beautify_string(colnames(my_report))
if (!max(my_report$CladeReads) > 1000) {
my_report[,c("CladeReads", "TaxonReads")] <- signif(my_report[,c("CladeReads", "TaxonReads")], digits = 4)
}
dt <- DT::datatable(my_report,
filter = 'bottom', selection = 'single',
class = datatable_opts$class,
extensions = datatable_opts$extensions,
escape = FALSE, rownames = FALSE,
options = list(buttons = common_buttons(input$sample_selector[1], "results"),
columnDefs=list(list(targets = seq(from=, to=2), visible=TRUE, orderSequence = c('desc','asc'))))
)
if (max(my_report$CladeReads) > 1000) {
dt <- dt %>% DT::formatCurrency(c("CladeReads", "TaxonReads"), digits = 0, currency = "")
}
dt %>%
DT::formatStyle(c("CladeReads","TaxonReads"),
background = styleColorBar2(c(0,my_report$CladeReads,na.rm=T), 'lightblue')) %>%
DT::formatString(c("Percentage"), suffix = '%') %>%
DT::formatStyle(c("Percentage"),
background = styleColorBar2(c(0,100,na.rm=T), 'lightblue'))
}, server = TRUE)
output$downloadData <- downloadHandler(
filename = function() { sprintf("%s-report-%s.tsv", input$sample_selector[1], format(Sys.time(), "%y%m%d")) },
content = function(file) {
utils::write.table(beautify_colnames(sample_view_report()), file, row.names = FALSE, sep = "\t")
}
)
## When a row (i.e. a taxonomical entry) gets selected in the sample view table, an action button appears to view the species in the overview
output$view_in_samples_comparison <- renderUI({
req(input$dt_sample_view_rows_selected)
selected_row <- input$dt_sample_view_rows_selected
my_report <- sample_view_report()
selected_sample <-
my_report[input$dt_sample_view_rows_selected, "name"]
selected_sample <- sub("^u_", "", selected_sample)
selected_sample <- sub("^-_", "", selected_sample)
selected_sample <- sub("^d_", "domain ", selected_sample)
selected_sample <- sub("^k_", "kingdom ", selected_sample)
selected_sample <- sub("^p_", "phylum ", selected_sample)
selected_sample <- sub("^o_", "order ", selected_sample)
selected_sample <- sub("^f_", "family ", selected_sample)
selected_sample <- sub("^g_", "genus ", selected_sample)
selected_sample <- sub("^s_", "species ", selected_sample)
## TODO: Add a custom search functionality
#actionButton("view_selected_in_samples_comparison",paste("--> View abundances of ",selected_sample,"across samples"))
})
output$blastn <- renderUI({
req(tbx_results_df())
#str(tbx_results_df())
## TODO: Add a custom search functionality
#actionButton("view_selected_in_samples_comparison",paste("--> View abundances of ",selected_sample,"across samples"))
})
observeEvent(input$view_selected_in_samples_comparison, {
my_report <- sample_view_report()
selected_sample <-
my_report[input$dt_sample_view_rows_selected, "name"]
updateTabsetPanel(session, "main_page", selected = "Sample comparison")
}, ignoreNULL = TRUE)
## D3partitionR does not display - might be added back at a later point in time
# output$D3partionR <- D3partitionR::renderD3partitionR({
# library(D3partitionR)
# my_report <- sample_view_report()
# my_report <- my_report[my_report$cladeReads > 0 & my_report$taxonReads > 10 & grepl("^._root",my_report$taxLineage), ]
# #taxLineage <- sub("^._root.","",my_report$taxLineage) %>% gsub("._","", .)
# strsplit(my_report$taxLineage, "|", fixed=T) %>% lapply(grep, pattern= "^-_", invert = T, value = T)
#
# domains <- c("d", "p", "c", "f", "g", "s")
# pattern <- sprintf("^[%s]_", paste(domains, collapse=""))
# res <- strsplit(my_report$taxLineage, "|", fixed=T) %>%
# lapply(function(x) {
# y <- grep(pattern, x, value = T)
# d <- sub("_.*", "", y)
# n <- sub("^._", "", y)
# names(n) <- d
# #xx <- n[domains]
# #xx[is.na(xx)] <- "NA"
# #xx
# n[domains]
# }) %>% do.call(rbind, .)
# colnames(res) <- domains
# res <- data.frame(res, stringsAsFactors = FALSE)
# sel <- !apply(is.na(res), 1, any) & my_report$taxonReads > 0
# #sel <- !apply(is.na(res), 1, all)
# #sel <- my_report$cladeReads
# res$N <- my_report$taxonRead
# res <- res[sel, ]
# library(plyr)
# res <- ddply(res, domains, function(x) {
# a = x[1, , drop=F]
# a$N = sum(x$N)
# a
# } )
#
# D3partitionR::D3partitionR() %>%
# D3partitionR::add_data(res, count = 'N', steps = domains, color='N') %>%
# #D3partitionR::add_title(list(text=input$sample_selector)) %>%
# set_chart_type(input$d3part_charttype) %>%
# plot
# })
#reactive({
# req(input$show_in_comparison)
# return(isolate(hover_plots$taxon));
#})
}
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