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| 1 | +#' The application server-side |
| 2 | +#' |
| 3 | +#' @param input,output,session Internal parameters for {shiny}. |
| 4 | +#' DO NOT REMOVE. |
| 5 | +#' @import shiny |
| 6 | +#' @import shinyjs |
| 7 | +#' @import dashboardthemes |
| 8 | +#' @import shinydashboard |
| 9 | +#' @import DT |
| 10 | +#' @import stringr |
| 11 | +#' @import tidyverse |
| 12 | +#' @import ComplexHeatmap |
| 13 | +#' @import InteractiveComplexHeatmap |
| 14 | +#' @import circlize |
| 15 | +#' @import shinythemes |
| 16 | +#' @import colourpicker |
| 17 | +#' @import shinyjqui |
| 18 | +#' @noRd |
| 19 | +app_server <- function( input, output, session ) { |
| 20 | + observeEvent(input$toggleSidebar, { |
| 21 | + shinyjs::toggle(id = "Sidebar") |
| 22 | + }) |
| 23 | + observeEvent(input$toggleSidebar2, { |
| 24 | + shinyjs::toggle(id = "Sidebar2") |
| 25 | + }) |
| 26 | + |
| 27 | + ## input dataframe |
| 28 | + raw_tbl <- reactive({ |
| 29 | + file1 <- input$input_df |
| 30 | + if(is.null(file1)){return()} |
| 31 | + read.table(file = file1$datapath, |
| 32 | + sep="\t", |
| 33 | + header = T, |
| 34 | + stringsAsFactors = F) |
| 35 | + }) |
| 36 | + ## raw df play |
| 37 | + output$Original_tbl = DT::renderDataTable({ |
| 38 | + if(is.null(raw_tbl())){return()} |
| 39 | + tbl1 <- as.data.frame(raw_tbl()) |
| 40 | + tbl1 |
| 41 | + }) |
| 42 | + |
| 43 | + clean<-reactiveValues(data=NULL) |
| 44 | + |
| 45 | + observeEvent( |
| 46 | + input$start_clean, |
| 47 | + { |
| 48 | + clean$na_tag = as.character(input$na_tag) |
| 49 | + clean$na_treat = as.character(input$na_treat) |
| 50 | + clean$na_replace = as.numeric(input$na_replace) |
| 51 | + clean$noise_remove = as.logical(input$noise_remove) |
| 52 | + clean$sample_percentage = as.numeric(input$sample_percentage) |
| 53 | + clean$noise_cutoff = as.numeric(input$noise_cutoff) |
| 54 | + clean$tbl <- Datacleaning(x = raw_tbl(), |
| 55 | + na_value_treat = clean$na_treat, |
| 56 | + na_tag = clean$na_tag, |
| 57 | + na_replace_value = clean$na_replace, |
| 58 | + remove_noise = clean$noise_remove, |
| 59 | + sample_percetage = clean$sample_percentage, |
| 60 | + noise_cutoff = clean$noise_cutoff) |
| 61 | + } |
| 62 | + ) |
| 63 | + |
| 64 | + output$Clean_tbl = DT::renderDataTable({ |
| 65 | + if(is.null(raw_tbl())){return()} |
| 66 | + if(is.null(clean$tbl)) {return()} |
| 67 | + clean$tbl |
| 68 | + }) |
| 69 | + |
| 70 | + norm<-reactiveValues(data=NULL) |
| 71 | + |
| 72 | + observeEvent( |
| 73 | + input$start_norm, |
| 74 | + { |
| 75 | + norm$norm_method = as.character(input$norm_method) |
| 76 | + norm$scale_method = as.character(input$scale_method) |
| 77 | + norm$p_data = getNormTable( |
| 78 | + x = clean$tbl, |
| 79 | + normlize = norm$norm_method, |
| 80 | + scale = norm$scale_method |
| 81 | + ) |
| 82 | + } |
| 83 | + ) |
| 84 | + output$norm_tbl = DT::renderDataTable({ |
| 85 | + if(is.null(norm$p_data)){return()} |
| 86 | + norm$p_data |
| 87 | + }) |
| 88 | + ## 03.basicHeatmap |
| 89 | + row_anno_tbl <- reactive({ |
| 90 | + file2 <- input$row_annotation |
| 91 | + if(is.null(file2)){return()} |
| 92 | + read.table(file = file2$datapath, |
| 93 | + sep="\t", |
| 94 | + header = T, |
| 95 | + stringsAsFactors = F) |
| 96 | + }) |
| 97 | + col_anno_tbl <- reactive({ |
| 98 | + file3 <- input$col_annotation |
| 99 | + if(is.null(file3)){return()} |
| 100 | + read.table(file = file3$datapath, |
| 101 | + sep="\t", |
| 102 | + header = T, |
| 103 | + stringsAsFactors = F) |
| 104 | + }) |
| 105 | + ## annotation |
| 106 | + basic<-reactiveValues(data=NULL) |
| 107 | + observeEvent( |
| 108 | + input$basicSetting, |
| 109 | + { |
| 110 | + ## annotation |
| 111 | + if (is.null(row_anno_tbl())) { |
| 112 | + basic$row_anno = NULL |
| 113 | + } else { |
| 114 | + basic$row_anno = row_anno_tbl() %>% |
| 115 | + column_to_rownames(colnames(row_anno_tbl())[1]) |
| 116 | + } |
| 117 | + if (is.null(col_anno_tbl())) { |
| 118 | + basic$col_anno = NULL |
| 119 | + } else { |
| 120 | + basic$col_anno = col_anno_tbl() %>% |
| 121 | + column_to_rownames(colnames(col_anno_tbl())[1]) |
| 122 | + } |
| 123 | + ## basic all |
| 124 | + basic$show_rownames = as.logical(input$show_rownames) |
| 125 | + basic$show_colnames = as.logical(input$show_colnames) |
| 126 | + ## color |
| 127 | + basic$break_min = as.numeric(input$break_min) |
| 128 | + basic$break_mid = as.numeric(input$break_mid) |
| 129 | + basic$break_max = as.numeric(input$break_max) |
| 130 | + basic$colormin= as.character(input$colormin) |
| 131 | + basic$colormid= as.character(input$colormid) |
| 132 | + basic$colormax= as.character(input$colormax) |
| 133 | + basic$row_anno_side = as.character(input$row_anno_side) |
| 134 | + basic$col_anno_side = as.character(input$col_anno_side) |
| 135 | + } |
| 136 | + ) |
| 137 | + hclust_list <- reactiveValues(data = NULL) |
| 138 | + observeEvent( |
| 139 | + input$start_hclust, |
| 140 | + { |
| 141 | + ## hclust |
| 142 | + hclust_list$cluster_row = as.logical(input$cluster_row) |
| 143 | + hclust_list$cluster_row_method = as.character(input$cluster_row_method) |
| 144 | + hclust_list$cluster_row_distance = as.character(input$cluster_row_distance) |
| 145 | + hclust_list$cluster_col= as.logical(input$cluster_col) |
| 146 | + hclust_list$cluster_col_method = as.character(input$cluster_col_method) |
| 147 | + hclust_list$cluster_col_distance = as.character(input$cluster_col_distance) |
| 148 | + } |
| 149 | + ) |
| 150 | + |
| 151 | + |
| 152 | + ht_list = reactive({ |
| 153 | + p = ComplexHeatmap::Heatmap( |
| 154 | + matrix = as.matrix(norm$p_data), |
| 155 | + show_row_names = basic$show_rownames, |
| 156 | + show_column_names = basic$show_colnames, |
| 157 | + cluster_rows = hclust_list$cluster_row, |
| 158 | + cluster_columns = hclust_list$cluster_col, |
| 159 | + clustering_distance_columns = hclust_list$cluster_col_distance, |
| 160 | + clustering_distance_rows = hclust_list$cluster_row_distance, |
| 161 | + clustering_method_columns = hclust_list$cluster_col_method, |
| 162 | + clustering_method_rows = hclust_list$cluster_row_method, |
| 163 | + col = colorRamp2(c(basic$break_min, basic$break_mid, basic$break_max),c(basic$colormin, basic$colormid, basic$colormax)) |
| 164 | + ) |
| 165 | + p.final = getFinalHeatmap( |
| 166 | + basicPlot = p, |
| 167 | + row_anno_side = basic$row_anno_side, |
| 168 | + col_anno_side = basic$col_anno_side, |
| 169 | + anno_row = basic$row_anno, |
| 170 | + anno_col = basic$col_anno |
| 171 | + ) |
| 172 | + draw(p.final) |
| 173 | + }) |
| 174 | + |
| 175 | + observeEvent(input$get_hclust,{ |
| 176 | + if(is.null(norm$p_data)){return()} |
| 177 | + InteractiveComplexHeatmapModal(input,output,session,ht_list()) |
| 178 | + }) |
| 179 | + |
| 180 | + kmeans_list <- reactiveValues(data = NULL) |
| 181 | + observeEvent( |
| 182 | + input$start_kmeans, |
| 183 | + { |
| 184 | + ## kmeans |
| 185 | + kmeans_list$km_row = as.numeric(input$km_row) |
| 186 | + kmeans_list$km_col = as.numeric(input$km_col) |
| 187 | + kmeans_list$km_repeat_time = as.numeric(input$km_repeat_time) |
| 188 | + } |
| 189 | + ) |
| 190 | + |
| 191 | + ht_list1 = reactive({ |
| 192 | + p2 = ComplexHeatmap::Heatmap( |
| 193 | + matrix = as.matrix(norm$p_data), |
| 194 | + show_row_names = basic$show_rownames, |
| 195 | + show_column_names = basic$show_colnames, |
| 196 | + column_km = kmeans_list$km_col, |
| 197 | + row_km = kmeans_list$km_row, |
| 198 | + row_km_repeats = kmeans_list$km_repeat_time, |
| 199 | + column_km_repeats = kmeans_list$km_repeat_time, |
| 200 | + col = colorRamp2(c(basic$break_min, basic$break_mid, basic$break_max), c(basic$colormin, basic$colormid, basic$colormax)) |
| 201 | + ) |
| 202 | + p.final2 = getFinalHeatmap( |
| 203 | + basicPlot = p2, |
| 204 | + row_anno_side = basic$row_anno_side, |
| 205 | + col_anno_side = basic$col_anno_side, |
| 206 | + anno_row = basic$row_anno, |
| 207 | + anno_col = basic$col_anno |
| 208 | + ) |
| 209 | + draw(p.final2) |
| 210 | + }) |
| 211 | + |
| 212 | + observeEvent(input$get_kmeans,{ |
| 213 | + if(is.null(norm$p_data)){return()} |
| 214 | + InteractiveComplexHeatmapModal(input,output,session,ht_list1()) |
| 215 | + }) |
| 216 | +} |
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