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1 changed files with 104 additions and 79 deletions
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@ -44,7 +44,110 @@ function(input, output, session) {
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, color = "green")
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)
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})
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observeEvent(
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{
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input$switch_target
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input$snp_ligand_dist
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input$snp_nca_dist
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input$snp_interface_dist
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},{
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target_gene = input$switch_target
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merged_df3 = cbind(get(paste0(input$switch_target, '_merged_df3')))
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position_max=max(merged_df3[['position']])
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position_min=min(merged_df3[['position']])
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min_ligand_distance=min(merged_df3$ligand_distance)
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max_ligand_distance=max(merged_df3$ligand_distance)
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# FIXME: these are IMPORTANT
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# # add "pos_count" position count column
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# merged_df3=merged_df3 %>% dplyr::add_count(position)
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# merged_df3$pos_count=merged_df3$n
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# merged_df3$n=NULL
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#
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mutable_df3 = cbind(merged_df3)
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#### site_snp_count_bp ####
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#mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
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# ligand_distance
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# interface_dist
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# nca_distance
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# change to: multiple plots, all use site_snp_count_bp
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# 4 x plots side by side, one normal (no dist. filter), 2/3 filtered by distance columns above
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# use "subtitle text" from pos_count_bp_i.R
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# different data ranges required for SNP distances
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snp_ligand_dist_df3 = merged_df3[merged_df3[['ligand_distance']]<input$snp_ligand_dist,]
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if ("interface_dist" %in% colnames(merged_df3)){
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snp_interface_dist_df3 = merged_df3[merged_df3[['interface_dist']]<input$snp_interface_dist,]
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} else {
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snp_interface_dist_df3 = NULL
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}
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if ("nca_distance" %in% colnames(merged_df3)){
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snp_nca_dist_df3 = merged_df3[merged_df3[['nca_distance']]<input$snp_nca_dist,]
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} else {
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snp_nca_dist_df3 = NULL
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}
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output$site_snp_count_bp = renderPlot(
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site_snp_count_bp(
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mutable_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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)
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output$site_snp_count_bp_ligand = renderPlot(
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site_snp_count_bp(
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snp_ligand_dist_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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)
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# if ("interface_dist" %in% colnames(input$switch_target)) {
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output$site_snp_count_interface = renderPlot(
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site_snp_count_bp(
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snp_interface_dist_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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)
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# } #else {
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# output$site_snp_count_interface = renderPlot(
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# ggplot() + annotate(x=1,y=1,"text", label="No interface data for this target")+theme_void()
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# )
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# }
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output$site_snp_count_nca = renderPlot( #{
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#if ("nca_distance" %in% colnames(input$switch_target)) {
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site_snp_count_bp(
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snp_nca_dist_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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# } else {
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# ggplot() + annotate(x=1,y=1,"text", label="No RNA data for this target")+theme_void()
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# }
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# }
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)
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}
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)
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observeEvent(
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{
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input$display_position_range
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@ -52,9 +155,6 @@ function(input, output, session) {
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input$logoplot_colour_scheme
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input$omit_snp_count
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input$switch_target
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input$snp_ligand_dist
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input$snp_nca_dist
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input$snp_interface_dist
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input$force
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},
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{
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@ -122,19 +222,6 @@ function(input, output, session) {
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updateNumericInput(session, "snp_nca_dist", min = min(merged_df3$nca_distance), max = max(merged_df3$nca_distance))
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# different data ranges required for SNP distances
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snp_ligand_dist_df3 = merged_df3[merged_df3[['ligand_distance']]<input$snp_ligand_dist,]
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if ("interface_dist" %in% colnames(merged_df3)){
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snp_interface_dist_df3 = merged_df3[merged_df3[['interface_dist']]<input$snp_interface_dist,]
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} else {
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snp_interface_dist_df3 = NULL
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}
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if ("nca_distance" %in% colnames(merged_df3)){
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snp_nca_dist_df3 = merged_df3[merged_df3[['nca_distance']]<input$snp_nca_dist,]
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} else {
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snp_nca_dist_df3 = NULL
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}
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stability_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
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outcome_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
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@ -242,68 +329,6 @@ function(input, output, session) {
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)
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)
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#### site_snp_count_bp ####
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#mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
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# ligand_distance
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# interface_dist
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# nca_distance
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# change to: multiple plots, all use site_snp_count_bp
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# 4 x plots side by side, one normal (no dist. filter), 2/3 filtered by distance columns above
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# use "subtitle text" from pos_count_bp_i.R
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output$site_snp_count_bp = renderPlot(
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site_snp_count_bp(
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mutable_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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)
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output$site_snp_count_bp_ligand = renderPlot(
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site_snp_count_bp(
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snp_ligand_dist_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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)
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# if ("interface_dist" %in% colnames(input$switch_target)) {
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output$site_snp_count_interface = renderPlot(
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site_snp_count_bp(
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snp_interface_dist_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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)
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# } #else {
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# output$site_snp_count_interface = renderPlot(
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# ggplot() + annotate(x=1,y=1,"text", label="No interface data for this target")+theme_void()
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# )
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# }
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output$site_snp_count_nca = renderPlot( #{
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#if ("nca_distance" %in% colnames(input$switch_target)) {
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site_snp_count_bp(
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snp_nca_dist_df3,
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title_colour = 'black',
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subtitle_colour = "black",
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leg_text_size = 12,
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axis_label_size = 12,
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geom_ls = 4
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)
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# } else {
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# ggplot() + annotate(x=1,y=1,"text", label="No RNA data for this target")+theme_void()
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# }
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# }
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)
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