diff --git a/drug-target/global.R b/drug-target/global.R index 2418223..354dc78 100644 --- a/drug-target/global.R +++ b/drug-target/global.R @@ -312,343 +312,343 @@ if (interactive()){ options(DT.options = list(scrollX = TRUE)) #### UI #### ui <- dashboardPage(skin="purple", - dashboardHeader(title = "Drug/Target Explorer"), - - dashboardSidebar( - sidebarMenu( id = "sidebar", - selectInput( - "switch_target", - label="Switch to New Target", - choices = c( - "alr", - "embb", - "gid", - "katg", - "pnca", - "rpob" - ), - selected="embb"), - menuItem("LogoP SNP", tabName="LogoP SNP"), - #menuItem("Lineage Sample Count", tabName="Lineage Sample Count"), - menuItem("Site SNP count", tabName="Site SNP count"), - menuItem("Stability SNP by site", tabName="Stability SNP by site"), - menuItem("DM OM Plots", tabName="DM OM Plots"), - menuItem("Correlation", tabName="Correlation"), - #menuItem("Lineage Distribution", tabName="Lineage Distribution"), - menuItem("Consurf", tabName="Consurf"), - menuItem("LogoP OR", tabName="LogoP OR"), - menuItem("Lineage", tabName="Lineage"), - #menuItem('Stability count', tabName='Stability count'), - - # These conditionalPanel()s make extra settings appear in the sidebar when needed - conditionalPanel( - condition="input.sidebar == 'LogoP SNP'", - textInput( - "omit_snp_count", - "Omit SNPs", - value = c(0), - placeholder = "1,3,6" - ) - ), - # NOTE: - # I *think* we can cheat here slightly and use the min/max from - # merged_df3[['position']] for everything because the various - # dataframes for a given gene/drug combination have the - # same range of positions. May need fixing, especially - # if we get/shrink the imported data files to something - # more reasonable. - conditionalPanel( - condition=" + dashboardHeader(title = "Drug/Target Explorer"), + + dashboardSidebar( + sidebarMenu( id = "sidebar", + selectInput( + "switch_target", + label="Switch to New Target", + choices = c( + "alr", + "embb", + "gid", + "katg", + "pnca", + "rpob" + ), + selected="embb"), + menuItem("LogoP SNP", tabName="LogoP SNP"), + #menuItem("Lineage Sample Count", tabName="Lineage Sample Count"), + menuItem("Site SNP count", tabName="Site SNP count"), + menuItem("Stability SNP by site", tabName="Stability SNP by site"), + menuItem("DM OM Plots", tabName="DM OM Plots"), + menuItem("Correlation", tabName="Correlation"), + #menuItem("Lineage Distribution", tabName="Lineage Distribution"), + menuItem("Consurf", tabName="Consurf"), + menuItem("LogoP OR", tabName="LogoP OR"), + menuItem("Lineage", tabName="Lineage"), + #menuItem('Stability count', tabName='Stability count'), + + # These conditionalPanel()s make extra settings appear in the sidebar when needed + conditionalPanel( + condition="input.sidebar == 'LogoP SNP'", + textInput( + "omit_snp_count", + "Omit SNPs", + value = c(0), + placeholder = "1,3,6" + ) + ), + # NOTE: + # I *think* we can cheat here slightly and use the min/max from + # merged_df3[['position']] for everything because the various + # dataframes for a given gene/drug combination have the + # same range of positions. May need fixing, especially + # if we get/shrink the imported data files to something + # more reasonable. + conditionalPanel( + condition=" input.sidebar == 'LogoP SNP'|| input.sidebar == 'Stability SNP by site' || input.sidebar == 'Consurf' || input.sidebar == 'LogoP OR'", - sliderInput( - "display_position_range" - , "Display Positions" - , min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count - ) - ), - - conditionalPanel( - condition=" + sliderInput( + "display_position_range" + , "Display Positions" + , min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count + ) + ), + + conditionalPanel( + condition=" input.sidebar == 'LogoP SNP' || input.sidebar == 'LogoP OR' || input.sidebar == 'LogoP ED'", - selectInput( - "logoplot_colour_scheme", - label="Logo Plot Colour Scheme", - choices = logoPlotSchemes, - selected="chemistry" - ) - ), - conditionalPanel( - condition="input.sidebar == 'Correlation'", - selectInput( - "corr_method", - label="Correlation Method", - choices = list("spearman", - "pearson", - "kendall"), - selected="spearman" - ) - ), - conditionalPanel( - condition="input.sidebar == 'Correlation'", - numericInput( - "corr_lig_dist" - , "Ligand Distance Cutoff (Å)", value=1 - ) - ), - conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - numericInput( - "snp_ligand_dist" - , "Ligand Distance Cutoff (Å)", value=10 - ) - ), - conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - numericInput( - "snp_interface_dist" - , "Interface Distance Cutoff (Å)", value=10 - ) - ), - conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - numericInput( - "snp_nca_dist" - , "NCA Distance Cutoff (Å)", value=10 - ) - ), - - conditionalPanel( - condition="input.sidebar == 'Correlation'", - checkboxGroupInput( - "corr_selected", - "Parameters", - choiceNames = c( - "DeepDDG", - "Dynamut2", - "FoldX", - "ConSurf"#, - ), - choiceValues = c( - "DeepDDG", - "Dynamut2", - "FoldX", - "ConSurf"#, - ), - selected = c( - "DeepDDG", - "Dynamut2", - "FoldX", - "ConSurf"#, - ) - ) - ), - - # conditionalPanel( - # condition="input.sidebar == 'DM OM Plots'", - # selectInput( - # "dm_om_param", - # label="Stability Parameter", - # choices = keys(dm_om_map), - # selected="SNAP2") - # ), - # colour_categ - conditionalPanel( - condition="input.sidebar == 'Stability SNP by site'", - selectInput( - "stability_snp_param", - label="Stability Parameter", - choices = stability_boxes_df$stability_type, - selected="Average") - ), - conditionalPanel( - condition="input.sidebar == 'Stability SNP by site'", - checkboxInput("reorder_custom_h", - label="Reorder by SNP count", - FALSE) - ), - conditionalPanel( - condition="input.sidebar.match(/^Lineage.*/)", - checkboxInput("all_lineages", - label="All Lineages", - FALSE) - ), - # an example of how you can match multiple things in frontend JS - conditionalPanel( - condition="input.sidebar == 'LogoP SNP' || + selectInput( + "logoplot_colour_scheme", + label="Logo Plot Colour Scheme", + choices = logoPlotSchemes, + selected="chemistry" + ) + ), + conditionalPanel( + condition="input.sidebar == 'Correlation'", + selectInput( + "corr_method", + label="Correlation Method", + choices = list("spearman", + "pearson", + "kendall"), + selected="spearman" + ) + ), + conditionalPanel( + condition="input.sidebar == 'Correlation'", + numericInput( + "corr_lig_dist" + , "Ligand Distance Cutoff (Å)", value=1 + ) + ), + conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + numericInput( + "snp_ligand_dist" + , "Ligand Distance Cutoff (Å)", value=10 + ) + ), + conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + numericInput( + "snp_interface_dist" + , "Interface Distance Cutoff (Å)", value=10 + ) + ), + conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + numericInput( + "snp_nca_dist" + , "NCA Distance Cutoff (Å)", value=10 + ) + ), + + conditionalPanel( + condition="input.sidebar == 'Correlation'", + checkboxGroupInput( + "corr_selected", + "Parameters", + choiceNames = c( + "DeepDDG", + "Dynamut2", + "FoldX", + "ConSurf"#, + ), + choiceValues = c( + "DeepDDG", + "Dynamut2", + "FoldX", + "ConSurf"#, + ), + selected = c( + "DeepDDG", + "Dynamut2", + "FoldX", + "ConSurf"#, + ) + ) + ), + + # conditionalPanel( + # condition="input.sidebar == 'DM OM Plots'", + # selectInput( + # "dm_om_param", + # label="Stability Parameter", + # choices = keys(dm_om_map), + # selected="SNAP2") + # ), + # colour_categ + conditionalPanel( + condition="input.sidebar == 'Stability SNP by site'", + selectInput( + "stability_snp_param", + label="Stability Parameter", + choices = stability_boxes_df$stability_type, + selected="Average") + ), + conditionalPanel( + condition="input.sidebar == 'Stability SNP by site'", + checkboxInput("reorder_custom_h", + label="Reorder by SNP count", + FALSE) + ), + conditionalPanel( + condition="input.sidebar.match(/^Lineage.*/)", + checkboxInput("all_lineages", + label="All Lineages", + FALSE) + ), + # an example of how you can match multiple things in frontend JS + conditionalPanel( + condition="input.sidebar == 'LogoP SNP' || input.sidebar =='Stability SNP by site' || input.sidebar =='Consurf' || input.sidebar =='LogoP OR'", - actionButton("clear_ngl", - "Clear Structure") - ), - conditionalPanel( - condition="input.sidebar == 'LogoP SNP' || + actionButton("clear_ngl", + "Clear Structure") + ), + conditionalPanel( + condition="input.sidebar == 'LogoP SNP' || input.sidebar =='Stability SNP by site' || input.sidebar =='Consurf' || input.sidebar =='LogoP OR'", - actionButton("test_ngl", - "Test NGLViewR") - )#, - - # downloadButton("save", - # "Download Plot" - # ) - # actionButton( - # "reload_target", - # label="Reload Target\nData (slow!)" - # ) - - ) - ), - #### body #### - body <- dashboardBody( - - tabItems( - tabItem(tabName = "dashboard", - h2("Dashboard tab content") - ), - - tabItem(tabName = "widgets", - h2("Widgets tab content") - ) - ), - # creates a 'Conditional Panel' containing a plot object from each of our - # ggplot plot functions (and its associated data frame) - fluidRow(column(width=12, - lapply(plot_functions_df$tab_name, - function(x){ - - plot_function=plot_functions_df[ - plot_functions_df$tab_name==x, - "plot_function"] - - plot_df=plot_functions_df[ - plot_functions_df$tab_name==x, - "plot_df"] - cat(paste0('\nCreating output: ', x)) - generate_conditionalPanel(x, plot_function, plot_df) - - } - ) - ) - ), - # Explicit fluidRow() for Lineage plots together - fluidRow( - column(conditionalPanel( - condition="input.sidebar.match(/^Lineage.*/)", box( - title="Lineage Distribution" - , status = "info" - , width=NULL - , plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"), - height=800 - ) - ), width=6 - ), - column(conditionalPanel( - condition="input.sidebar.match(/^Lineage.*/)", box( - title="Lineage SNP Diversity" - , status = "info" - , width=NULL - , plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"), - height=800 - ) - ), width=6 - ) - - ), - # Explicit fluidRow() for Site SNP Count - fluidRow( - column(conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - box( - title="Site SNP count" - , status = "info" - , width=NULL - , plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1") - ) - ), width=6 - ), - column(conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - box( - title="Ligand Distance" - , status = "info" - , width=NULL - , plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1") - ) - ), width=6 - ), - column(conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - box( - title="Interface Distance" - , status = "info" - , width=NULL - , plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1") - ) - ), width=6 - ), - column(conditionalPanel( - condition="input.sidebar == 'Site SNP count'", - box( - title="RNA Distance" - , status = "info" - , width=NULL - , plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1") - ) - ), width=6 - ) - ), - - # # Explicit fluidRow() for Stability Count - # fluidRow( - # column( - # conditionalPanel( - # condition="input.sidebar.match(/^Lineage.*/)", - # lapply( - # # FIXME: using a hardcoded target DF for this IS WRONG AND WILL BREAK - # stability_boxes_df[stability_boxes_df$outcome_colname %in% colnames(embb_merged_df3),"outcome_colname"], - # function(x){ - # print(paste0("outcome_colname: ",x)) - # box(plotOutput(x), width=4) - # } - # ), - # width=12 - # ) - # ) - # ), - - #### fluidRow()s for "Stability Count" in the sidebar #### - fluidRow( - conditionalPanel( - condition=" + actionButton("test_ngl", + "Test NGLViewR") + )#, + + # downloadButton("save", + # "Download Plot" + # ) + # actionButton( + # "reload_target", + # label="Reload Target\nData (slow!)" + # ) + + ) + ), + #### body #### + body <- dashboardBody( + + tabItems( + tabItem(tabName = "dashboard", + h2("Dashboard tab content") + ), + + tabItem(tabName = "widgets", + h2("Widgets tab content") + ) + ), + # creates a 'Conditional Panel' containing a plot object from each of our + # ggplot plot functions (and its associated data frame) + fluidRow(column(width=12, + lapply(plot_functions_df$tab_name, + function(x){ + + plot_function=plot_functions_df[ + plot_functions_df$tab_name==x, + "plot_function"] + + plot_df=plot_functions_df[ + plot_functions_df$tab_name==x, + "plot_df"] + cat(paste0('\nCreating output: ', x)) + generate_conditionalPanel(x, plot_function, plot_df) + + } + ) + ) + ), + # Explicit fluidRow() for Lineage plots together + fluidRow( + column(conditionalPanel( + condition="input.sidebar.match(/^Lineage.*/)", box( + title="Lineage Distribution" + , status = "info" + , width=NULL + , plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"), + height=800 + ) + ), width=6 + ), + column(conditionalPanel( + condition="input.sidebar.match(/^Lineage.*/)", box( + title="Lineage SNP Diversity" + , status = "info" + , width=NULL + , plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"), + height=800 + ) + ), width=6 + ) + + ), + # Explicit fluidRow() for Site SNP Count + fluidRow( + column(conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + box( + title="Site SNP count" + , status = "info" + , width=NULL + , plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1") + ) + ), width=6 + ), + column(conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + box( + title="Ligand Distance" + , status = "info" + , width=NULL + , plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1") + ) + ), width=6 + ), + column(conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + box( + title="Interface Distance" + , status = "info" + , width=NULL + , plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1") + ) + ), width=6 + ), + column(conditionalPanel( + condition="input.sidebar == 'Site SNP count'", + box( + title="RNA Distance" + , status = "info" + , width=NULL + , plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1") + ) + ), width=6 + ) + ), + + # # Explicit fluidRow() for Stability Count + # fluidRow( + # column( + # conditionalPanel( + # condition="input.sidebar.match(/^Lineage.*/)", + # lapply( + # # FIXME: using a hardcoded target DF for this IS WRONG AND WILL BREAK + # stability_boxes_df[stability_boxes_df$outcome_colname %in% colnames(embb_merged_df3),"outcome_colname"], + # function(x){ + # print(paste0("outcome_colname: ",x)) + # box(plotOutput(x), width=4) + # } + # ), + # width=12 + # ) + # ) + # ), + + #### fluidRow()s for "Stability Count" in the sidebar #### + fluidRow( + conditionalPanel( + condition=" input.sidebar == 'LogoP SNP' || input.sidebar =='Stability SNP by site' || input.sidebar =='Consurf' || input.sidebar =='LogoP OR'", - column(NGLVieweROutput("structure"), - width=3 - ) - ), - conditionalPanel( - condition=" + column(NGLVieweROutput("structure"), + width=3 + ) + ), + conditionalPanel( + condition=" input.sidebar == 'LogoP SNP' || input.sidebar == 'Stability SNP by site' || input.sidebar == 'Site SNP count' || input.sidebar == 'Consurf' || input.sidebar == 'LogoP OR'", - column( - DT::dataTableOutput('table'), - width=9 + column( + DT::dataTableOutput('table'), + width=9 + ) + ) + ), ) - ) - ), - ) ) server <- function(input, output, session) { diff --git a/drug-target/server.R b/drug-target/server.R index 684c708..6526ee5 100644 --- a/drug-target/server.R +++ b/drug-target/server.R @@ -1,9 +1,3 @@ -# library(shiny) -# library(shinycssloaders) -# library(DT) -# library(NGLVieweR) -# library(hash) - function(input, output, session) { #output$LogoPlotSnps = renderPlot(LogoPlotSnps(mutable_df3)) diff --git a/drug-target/ui.R b/drug-target/ui.R index 041714f..e91a10e 100644 --- a/drug-target/ui.R +++ b/drug-target/ui.R @@ -1,10 +1,3 @@ -# library(shiny) -# library(shinydashboard) -# library(shinycssloaders) -# library(DT) -# library(NGLVieweR) -# library(hash) - #### Shiny UI ##### dashboardPage(skin="purple",