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f9db5cbc33
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27f70afb2c
2 changed files with 350 additions and 325 deletions
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@ -124,9 +124,18 @@ function(input, output, session) {
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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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snp_interface_dist_df3 = merged_df3[merged_df3$interface_dist<input$snp_interface_dist,]
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snp_nca_dist_df3 = merged_df3[merged_df3$nca_distance<input$snp_nca_dist,]
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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$stability_snp_param,"outcome_colname"]
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@ -162,7 +171,8 @@ function(input, output, session) {
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### NGLViewer ####
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# Structure Viewer WebGL/NGLViewR window
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output$structure <- renderNGLVieweR({
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ngl_gene=isolate(input$switch_target)
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#ngl_gene=isolate(input$switch_target)
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ngl_gene=input$switch_target
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ngl_drug=target_map[[ngl_gene]]
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ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
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print(ngl_pdb_file)
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@ -262,6 +272,8 @@ function(input, output, session) {
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geom_ls = 4
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)
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)
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# if ("interface_dist" %in% colnames(input$switch_target)) {
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output$site_snp_count_interface = renderPlot(
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site_snp_count_bp(
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snp_interface_dist_df3,
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@ -272,7 +284,14 @@ function(input, output, session) {
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geom_ls = 4
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)
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)
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output$site_snp_count_nca = renderPlot(
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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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@ -281,8 +300,14 @@ function(input, output, session) {
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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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#### DM OM Plots ####
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#dm_om_param
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# order needs to be:
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628
drug-target/ui.R
628
drug-target/ui.R
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@ -8,341 +8,341 @@
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#### Shiny UI #####
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dashboardPage(skin="purple",
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dashboardHeader(title = "Drug/Target Explorer"),
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dashboardHeader(title = "Drug/Target Explorer"),
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dashboardSidebar(
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sidebarMenu( id = "sidebar",
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selectInput(
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"switch_target",
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label="Switch to New Target",
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choices = c(
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"alr",
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"embb",
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"gid",
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"katg",
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"pnca",
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"rpob"
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),
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selected="embb"),
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menuItem("LogoP SNP", tabName="LogoP SNP"),
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#menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
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menuItem("Site SNP count", tabName="Site SNP count"),
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menuItem("Stability SNP by site", tabName="Stability SNP by site"),
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menuItem("DM OM Plots", tabName="DM OM Plots"),
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menuItem("Correlation", tabName="Correlation"),
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#menuItem("Lineage Distribution", tabName="Lineage Distribution"),
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menuItem("Consurf", tabName="Consurf"),
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menuItem("LogoP OR", tabName="LogoP OR"),
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menuItem("Lineage", tabName="Lineage"),
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#menuItem('Stability count', tabName='Stability count'),
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dashboardSidebar(
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sidebarMenu( id = "sidebar",
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selectInput(
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"switch_target",
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label="Switch to New Target",
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choices = c(
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"alr",
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"embb",
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"gid",
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"katg",
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"pnca",
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"rpob"
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),
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selected="embb"),
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menuItem("LogoP SNP", tabName="LogoP SNP"),
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#menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
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menuItem("Site SNP count", tabName="Site SNP count"),
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menuItem("Stability SNP by site", tabName="Stability SNP by site"),
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menuItem("DM OM Plots", tabName="DM OM Plots"),
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menuItem("Correlation", tabName="Correlation"),
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#menuItem("Lineage Distribution", tabName="Lineage Distribution"),
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menuItem("Consurf", tabName="Consurf"),
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menuItem("LogoP OR", tabName="LogoP OR"),
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menuItem("Lineage", tabName="Lineage"),
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#menuItem('Stability count', tabName='Stability count'),
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# These conditionalPanel()s make extra settings appear in the sidebar when needed
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP'",
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textInput(
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"omit_snp_count",
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"Omit SNPs",
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value = c(0),
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placeholder = "1,3,6"
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)
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),
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# NOTE:
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# I *think* we can cheat here slightly and use the min/max from
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# merged_df3[['position']] for everything because the various
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# dataframes for a given gene/drug combination have the
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# same range of positions. May need fixing, especially
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# if we get/shrink the imported data files to something
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# more reasonable.
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conditionalPanel(
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condition="
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# These conditionalPanel()s make extra settings appear in the sidebar when needed
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP'",
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textInput(
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"omit_snp_count",
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"Omit SNPs",
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value = c(0),
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placeholder = "1,3,6"
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)
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),
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# NOTE:
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# I *think* we can cheat here slightly and use the min/max from
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# merged_df3[['position']] for everything because the various
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# dataframes for a given gene/drug combination have the
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# same range of positions. May need fixing, especially
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# if we get/shrink the imported data files to something
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# more reasonable.
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conditionalPanel(
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condition="
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input.sidebar == 'LogoP SNP'||
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input.sidebar == 'Stability SNP by site' ||
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input.sidebar == 'Consurf' ||
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input.sidebar == 'LogoP OR'",
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sliderInput(
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"display_position_range"
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, "Display Positions"
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, min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
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)
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),
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sliderInput(
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"display_position_range"
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, "Display Positions"
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, min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
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)
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),
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conditionalPanel(
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condition="
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conditionalPanel(
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condition="
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input.sidebar == 'LogoP SNP' ||
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input.sidebar == 'LogoP OR' ||
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input.sidebar == 'LogoP ED'",
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selectInput(
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"logoplot_colour_scheme",
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label="Logo Plot Colour Scheme",
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choices = logoPlotSchemes,
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selected="chemistry"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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selectInput(
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"corr_method",
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label="Correlation Method",
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choices = list("spearman",
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"pearson",
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"kendall"),
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selected="spearman"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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numericInput(
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"corr_lig_dist"
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, "Ligand Distance Cutoff (Å)", value=1
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_ligand_dist"
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, "Ligand Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_interface_dist"
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, "Interface Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_nca_dist"
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, "NCA Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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checkboxGroupInput(
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"corr_selected",
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"Parameters",
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choiceNames = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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),
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choiceValues = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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),
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selected = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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)
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)
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),
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# conditionalPanel(
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# condition="input.sidebar == 'DM OM Plots'",
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# selectInput(
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# "dm_om_param",
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# label="Stability Parameter",
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# choices = keys(dm_om_map),
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# selected="SNAP2")
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# ),
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# colour_categ
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conditionalPanel(
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condition="input.sidebar == 'Stability SNP by site'",
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selectInput(
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"stability_snp_param",
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label="Stability Parameter",
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choices = stability_boxes_df$stability_type,
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selected="Average")
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),
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conditionalPanel(
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condition="input.sidebar == 'Stability SNP by site'",
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checkboxInput("reorder_custom_h",
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label="Reorder by SNP count",
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FALSE)
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),
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conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)",
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checkboxInput("all_lineages",
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label="All Lineages",
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FALSE)
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),
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# an example of how you can match multiple things in frontend JS
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP' ||
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input.sidebar =='Stability SNP by site' ||
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input.sidebar =='Consurf' ||
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input.sidebar =='LogoP OR'",
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actionButton("clear_ngl",
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"Clear Structure")
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),
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP' ||
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input.sidebar =='Stability SNP by site' ||
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input.sidebar =='Consurf' ||
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input.sidebar =='LogoP OR'",
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actionButton("test_ngl",
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"Test NGLViewR")
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)#,
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# downloadButton("save",
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# "Download Plot"
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# )
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# actionButton(
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# "reload_target",
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# label="Reload Target\nData (slow!)"
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# )
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)
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),
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#### body ####
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body <- dashboardBody(
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tabItems(
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tabItem(tabName = "dashboard",
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h2("Dashboard tab content")
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),
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tabItem(tabName = "widgets",
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h2("Widgets tab content")
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)
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),
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# creates a 'Conditional Panel' containing a plot object from each of our
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# ggplot plot functions (and its associated data frame)
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fluidRow(column(width=12,
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lapply(plot_functions_df$tab_name,
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function(x){
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plot_function=plot_functions_df[
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plot_functions_df$tab_name==x,
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"plot_function"]
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plot_df=plot_functions_df[
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plot_functions_df$tab_name==x,
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"plot_df"]
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cat(paste0('\nCreating output: ', x))
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generate_conditionalPanel(x, plot_function, plot_df)
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}
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selectInput(
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"logoplot_colour_scheme",
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label="Logo Plot Colour Scheme",
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choices = logoPlotSchemes,
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selected="chemistry"
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)
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)
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),
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# Explicit fluidRow() for Lineage plots together
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fluidRow(
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column(conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)", box(
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title="Lineage Distribution"
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, status = "info"
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, width=NULL
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, plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"),
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height=800
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)", box(
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title="Lineage SNP Diversity"
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, status = "info"
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, width=NULL
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, plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"),
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height=800
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)
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), width=6
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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selectInput(
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"corr_method",
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label="Correlation Method",
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choices = list("spearman",
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"pearson",
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"kendall"),
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selected="spearman"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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numericInput(
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"corr_lig_dist"
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, "Ligand Distance Cutoff (Å)", value=1
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_ligand_dist"
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, "Ligand Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_interface_dist"
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, "Interface Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_nca_dist"
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, "NCA Distance Cutoff (Å)", value=10
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)
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),
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),
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# Explicit fluidRow() for Site SNP Count
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fluidRow(
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Site SNP count"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Ligand Distance"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Interface Distance"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="NCA Distance"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
|
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checkboxGroupInput(
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"corr_selected",
|
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"Parameters",
|
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choiceNames = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
|
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"ConSurf"#,
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),
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choiceValues = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
|
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"ConSurf"#,
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),
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selected = c(
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"DeepDDG",
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"Dynamut2",
|
||||
"FoldX",
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"ConSurf"#,
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)
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)
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),
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# # Explicit fluidRow() for Stability Count
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# fluidRow(
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# column(
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# conditionalPanel(
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# condition="input.sidebar.match(/^Lineage.*/)",
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||||
# 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
|
||||
# )
|
||||
# )
|
||||
# ),
|
||||
# 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$stability_type,
|
||||
selected="Average")
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Stability SNP by site'",
|
||||
checkboxInput("reorder_custom_h",
|
||||
label="Reorder by SNP count",
|
||||
FALSE)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)",
|
||||
checkboxInput("all_lineages",
|
||||
label="All Lineages",
|
||||
FALSE)
|
||||
),
|
||||
# an example of how you can match multiple things in frontend JS
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
actionButton("clear_ngl",
|
||||
"Clear Structure")
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
actionButton("test_ngl",
|
||||
"Test NGLViewR")
|
||||
)#,
|
||||
|
||||
#### fluidRow()s for "Stability Count" in the sidebar ####
|
||||
fluidRow(
|
||||
conditionalPanel(
|
||||
condition="
|
||||
# downloadButton("save",
|
||||
# "Download Plot"
|
||||
# )
|
||||
# actionButton(
|
||||
# "reload_target",
|
||||
# label="Reload Target\nData (slow!)"
|
||||
# )
|
||||
|
||||
)
|
||||
),
|
||||
#### body ####
|
||||
body <- dashboardBody(
|
||||
|
||||
tabItems(
|
||||
tabItem(tabName = "dashboard",
|
||||
h2("Dashboard tab content")
|
||||
),
|
||||
|
||||
tabItem(tabName = "widgets",
|
||||
h2("Widgets tab content")
|
||||
)
|
||||
),
|
||||
# creates a 'Conditional Panel' containing a plot object from each of our
|
||||
# ggplot plot functions (and its associated data frame)
|
||||
fluidRow(column(width=12,
|
||||
lapply(plot_functions_df$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
|
||||
)
|
||||
)
|
||||
),
|
||||
)
|
||||
)
|
||||
Loading…
Add table
Add a link
Reference in a new issue