## plot alpha diversity
plotAlphaBoxplotButton <- eventReactive(input$alpha_boxplot,{
alpha_div_boxplot(MAE = vals$MAE,
tax_level = input$taxl.alpha,
condition = input$select_alpha_div_condition,
alpha_metric = input$select_alpha_div_method)
})
output$AlphaDiversity <- renderPlotly({
plotAlphaBoxplotButton()
})
#
# # Alpha diversity table
# do_alpha_table <- function() {
# shinyInput <- vals$shiny.input
# physeq1 <- shinyInput$pstat
# if (input$taxl.alpha !="no rank") {
# physeq1 <- tax_glom(physeq1, input$taxl.alpha)
# }
# meta.data <- physeq1@sam_data
# meta.data$sample.name <- rownames(meta.data)
# meta.data$richness <- suppressWarnings(estimate_richness(physeq = physeq1, split = T, measures = input$select_alpha_div_method)[,1])
# colnames(meta.data)[which(colnames(meta.data) == input$select_alpha_div_condition)] <- "condition"
# rownames(meta.data) <- seq_len(nrow(meta.data))
# DT::datatable(meta.data %>% dplyr::select(sample.name, condition, richness))
# }
#
#
# plotAlphaBoxplotButton2 <- eventReactive(input$alpha_boxplot,{
# do_alpha_table()
# })
# output$table.alpha <- DT::renderDataTable({
# plotAlphaBoxplotButton2()
# })
#
# # Download alpha diversity table
# output$download_table_alpha <- downloadHandler(
# filename = function() { paste('Alpha_diversity_table', '.csv', sep='') },
# content = function(file) {
# shinyInput <- vals$shiny.input
# physeq1 <- shinyInput$pstat
# if (input$taxl.alpha !="no rank") {
# physeq1 <- tax_glom(physeq1, input$taxl.alpha)
# }
# meta.data <- physeq1@sam_data
# meta.data$sample.name <- rownames(meta.data)
# meta.data$richness <- suppressWarnings(estimate_richness(physeq = physeq1, split = T, measures = input$select_alpha_div_method)[,1])
# colnames(meta.data)[which(colnames(meta.data) == input$select_alpha_div_condition)] <- "condition"
# rownames(meta.data) <- seq_len(nrow(meta.data))
# meta.data <- as_tibble(meta.data)
# meta.data <- meta.data %>% select(sample.name, condition, richness)
# write.csv(data.frame(meta.data), file)
# }
# )
## do alpha diversity statistical test
plotAlphaBoxplotButton3 <- eventReactive(input$alpha_boxplot,{
do_alpha_div_test(MAE = vals$MAE,
tax_level = input$taxl.alpha,
condition = input$select_alpha_div_condition,
alpha_metric = input$select_alpha_div_method,
alpha_stat = input$select_alpha_stat_method)
})
output$alpha.stat.test <- DT::renderDataTable({
plotAlphaBoxplotButton3()
}, options = list(paging = TRUE,
scrollX = TRUE,
pageLength = 5,
sDom = '<"top">t<"bottom">ip'))
## beta diversity heatmap
plotBetaHeatmapServerButton <- eventReactive(input$beta_heatmap,{
diversity_beta_heatmap(MAE = vals$MAE,
tax_level = input$taxl.beta,
input_beta_method = input$beta_method,
input_bdhm_select_conditions = input$bdhm_select_conditions,
input_bdhm_sort_by = input$bdhm_sort_by)
})
output$BetaDiversityHeatmap <- renderPlotly({
plotBetaHeatmapServerButton()
})
## beta diversity boxplot
plotBetaBoxplotServerButton <- eventReactive(input$beta_boxplot,{
diversity_beta_boxplot(MAE = vals$MAE,
tax_level = input$taxl.beta,
input_beta_method = input$beta_method,
input_select_beta_condition = input$select_beta_condition)
})
output$BetaDiversityBoxplot <- renderPlotly({
plotBetaBoxplotServerButton()
})
plotBetaBoxplotServerButton3 <- eventReactive(input$beta_boxplot, {
diversity_beta_test(MAE = vals$MAE,
tax_level = input$taxl.beta,
input_beta_method = input$beta_method,
input_select_beta_condition = input$select_beta_condition,
input_select_beta_stat_method = input$select_beta_stat_method,
input_num_permutation_permanova = input$num_permutation_permanova)
})
output$beta.stat.test <- DT::renderDataTable({
plotBetaBoxplotServerButton3()
}, options = list(sDom = '<"top">t<"bottom">ip'))
plotBetaNMDSServerButton <- eventReactive(input$beta_NMDS, {
diversity_beta_NMDS(MAE = vals$MAE,
tax_level = input$taxl.beta,
input_beta_method = input$beta_method,
input_select_beta_condition = input$select_beta_condition_NMDS) #,
#input_select_beta_stat_method = input$select_beta_stat_method,
#input_num_permutation_permanova = input$num_permutation_permanova)
})
output$betaDiversityNMDSPlot <- renderPlot({
plotBetaNMDSServerButton()}
)
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