function(input, output, session) { observeEvent( { input$display_position_full_range #special-purpose for MSA input$logoplot_colour_scheme input$switch_target }, { # C O M P A T I B I L I T Y #gene=input$switch_target #drug=target_map[[gene]] merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3'))) position_max=max(merged_df3[['position']]) position_min=min(merged_df3[['position']]) min_ligand_distance=min(merged_df3$ligand_distance) max_ligand_distance=max(merged_df3$ligand_distance) # FIXME: these are IMPORTANT # # add "pos_count" position count column # merged_df3=merged_df3 %>% dplyr::add_count(position) # merged_df3$pos_count=merged_df3$n # merged_df3$n=NULL # mutable_df3 = cbind(merged_df3) unified_msa = get(paste0(input$switch_target, '_unified_msa')) # # # re-sort the dataframe according to position count sorted_df = cbind(merged_df3) sorted_df = sorted_df %>% arrange(pos_count) # outdir = paste0("~/git/Data/", drug, '/output/') indir = paste0("~/git/Data/", drug , "/input/") # # source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary... # source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") #### nasty special-purpose merged_df3 variants #### # FIXME: SLOW # corr_plotdf = corr_data_extract( # merged_df3 # , gene = gene # , drug = drug # , extract_scaled_cols = F # ) #input$stability_snp_param updateSliderInput( session, "display_position_range", min = position_min, max = position_max #, value = c(position_min, position_min+150) ) updateSliderInput( session, "display_position_full_range", min = 1, max = position_max #, # value = c(position_min, position_min+150) ) updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min) updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min) updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance) stability_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"] outcome_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"] display_position_range = input$display_position_range plot_min=display_position_range[1] plot_max=display_position_range[2] display_position_full_range = input$display_position_full_range full_range_min=display_position_full_range[1] full_range_max=display_position_full_range[2] logoplot_colour_scheme = input$logoplot_colour_scheme omit_snp_count = input$omit_snp_count print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max)) subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),] subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),] subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),] #### LogoPlotMSA/Logo Plot ED #### output$LogoPlotMSA = renderPlot( LogoPlotMSA(target=input$switch_target, plot_positions=full_range_min:full_range_max, my_logo_col = logoplot_colour_scheme, aa_pos_drug = aa_pos_drug, active_aa_pos = active_aa_pos, aa_pos_lig1 = aa_pos_lig1, aa_pos_lig2 = aa_pos_lig2, aa_pos_lig3 = aa_pos_lig3 ) ) } ) }