aaaaaaa
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1 changed files with 115 additions and 16 deletions
131
tb_host/app.R
131
tb_host/app.R
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@ -52,23 +52,34 @@ ui=dashboardPage(skin="purple",
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selected="alr" # "alr" is a value
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),
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actionButton("clear_ngl",
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"Clear Structures")
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"Reset Structures"),
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actionButton("all_mutations",
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"All Mutations")
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),
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dashboardBody(
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useShinyjs(),
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fluidRow(
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box(
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title="Crystallised Structure",
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width=5,
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column(
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NGLVieweROutput("structure"),
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width=12
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)
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),
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box(
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title="AlphaFold Structure",
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width=5,
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column(
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NGLVieweROutput("af_structure"),
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width=12
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)
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),
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box(
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title="AlphaFold Structure",
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title="Mutation Information",
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width=2,
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column(
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NGLVieweROutput("af_structure"),
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htmlOutput("information"),
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width=12
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)
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)
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@ -104,8 +115,8 @@ server <- function(input, output) {
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NGLVieweR(ngl_gene) %>%
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addRepresentation("cartoon",
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param = list(name = "cartoon",
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#color="tan"
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colorScheme = "bfactor",
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color="tan",
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#colorScheme = "bfactor",
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opacity = 1
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)
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) %>%
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@ -155,6 +166,7 @@ server <- function(input, output) {
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observeEvent(input$table_rows_selected,{
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#req(length(input$table_row_selected) > 0)
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mutation = as.character(unique_missense_genes[input$table_rows_selected,"hgvd_p"])
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chain = as.character(unique_missense_genes[input$table_rows_selected,"chain"])
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# what the absolute FUCK is this mess? I JUST WANT THE MATCH ASDLASJASDASHFKLJASDFK
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# coming down from the trees was a mistake, and abandoning Perl doubly so.
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clicked_position = regmatches(mutation, regexpr("[0-9]+", mutation, perl=TRUE))
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@ -163,22 +175,22 @@ server <- function(input, output) {
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NGLVieweR_proxy("structure") %>%
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#addSelection('ball+stick'
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addSelection('ball+stick'
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addSelection('spacefill'
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, param = list(
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name = "Pos"
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, sele = clicked_position
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, color = "green"
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, sele = trimws(paste0(clicked_position,':', chain))
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, color = "red"
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#, colorValue="00ff00"
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#, colorScheme="element"
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)
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)
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NGLVieweR_proxy("af_structure") %>%
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#addSelection('ball+stick'
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addSelection('ball+stick'
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addSelection('spacefill'
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, param = list(
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name = "Pos"
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, sele = clicked_position
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, color = "green"
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, color = "red"
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#, colorValue="00ff00"
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#, colorScheme="element"
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)
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@ -191,12 +203,37 @@ server <- function(input, output) {
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z_offSet = -1
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)
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NGLVieweR_proxy("structure") %>% updateZoomMove(
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center = clicked_position,
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zoom = clicked_position,
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center = trimws(paste0(clicked_position,':', chain)),
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zoom = trimws(paste0(clicked_position,':', chain)),
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duration = 1000, # animation time in ms
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z_offSet = -1
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)
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output$information <- renderUI({
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selected_gene=input$gene
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HTML(paste0("<strong>Mutation: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mutationinformation"]),"<br/>",
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"<strong>PDB ID: </strong>", as.character(genes[genes$Gene==selected_gene,"PDB"]),"<br/>",
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"<strong>AlphaFold ID: </strong>", as.character(genes[genes$Gene==selected_gene,"AF_PDB"]), "<br/>",
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"<strong>Ligand Distance: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ligand_distance"]), "<br/>",
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"<strong>mCSM Lig: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_lig"]), "<br/>",
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"<strong>mmCSM Lig: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mmcsm_lig"]), "<br/>",
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"<strong>mCSM DUET: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_duet"]), "<br/>",
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"<strong>FoldX: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_foldx"]), "<br/>",
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"<strong>DeepDDG: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_deepddg"]), "<br/>",
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"<strong>Dynamut2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"ddg_dynamut2"]), "<br/>",
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"<strong>mCSM PPI2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_ppi2_affinity"]), "<br/>",
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"<strong>Interface Distance: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"interface_dist"]), "<br/>",
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"<strong>mCSM NA: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mcsm_na_affinity"]), "<br/>",
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"<strong>Consurf: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"consurf_score"]), "<br/>",
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#"<strong>SNAP2: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"snap2_score"]), "<br/>",
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"<strong>SNAP2 Outcome: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"snap2_outcome"]), "<br/>",
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#"<strong>PROVEAN: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"provean_score"]), "<br/>",
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"<strong>PROVEAN Outcome: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"provean_outcome"]), "<br/>",
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"<strong>RSA: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"rsa"]), "<br/>",
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"<strong>Residue Depth: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"rd_values"]), "<br/>"
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)
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)
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})
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# output$debug <- renderPrint({
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# print(c(mutation, clicked_position))
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@ -207,9 +244,71 @@ server <- function(input, output) {
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input$clear_ngl
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}, {
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NGLVieweR_proxy("structure") %>%
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removeSelection("Pos")
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removeSelection("Pos") %>%
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removeSelection("all_mutations_surface") %>%
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updateVisibility("cartoon", TRUE) %>%
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removeSelection("all_mutations")
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NGLVieweR_proxy("af_structure") %>%
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removeSelection("Pos")
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removeSelection("Pos") %>%
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removeSelection("all_mutations_surface") %>%
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updateVisibility("cartoon", TRUE) %>%
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removeSelection("all_mutations")
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})
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# add a surface representation and highlight all mutations on it
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observeEvent(
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{
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input$all_mutations
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}, {
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gene = input$gene
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mutations = paste0(
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apply(
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unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
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1,
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function(x){
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paste0(trimws(x[1]),
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":",
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trimws(x[2])
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)}
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),
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collapse=","
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)
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print(mutations)
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NGLVieweR_proxy("structure") %>%
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updateVisibility("cartoon", FALSE) %>%
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addSelection(type="surface",
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param = list(name = "all_mutations_surface",
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sele = "all",
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color="tan",
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opacity = 0.2
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)
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) %>%
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addSelection(type="surface",
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param = list(name = "all_mutations",
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color="green",
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sele = "20:A, 22:A, 157:A"
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#colorScheme = "bfactor",
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#opacity = 1
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)
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)
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# addSelection('spacefill',
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# param = list(
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# name = "Pos",
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# sele = "4:A,20:A,22:A,157:A,344:A",
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# color = "red",
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# opacity=0.1
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# )
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# )
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# NGLVieweR_proxy("af_structure") %>%
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# addSelection('ball+stick',
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# param = list(
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# name = "Pos",
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# sele = mutations,
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# color = "red",
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# opacity=0.1
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# )
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# )
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})
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}
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