shuffle everything
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8c96f1a317
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48d9e88bc9
3 changed files with 60 additions and 16 deletions
29
global.R
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29
global.R
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@ -0,0 +1,29 @@
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library(dplyr)
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library(DT)
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library(ggplot2)
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library(grid) # for the info box
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library(plotly)
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library(NGLVieweR)
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library(httr)
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library(readr)
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library(RCurl)
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# make shiny non-stupid
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#options(shiny.launch.browser = FALSE) # i am a big girl and can tie my own laces
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#options(shiny.port = 8000) # don't change the port every time
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#options(shiny.host = '0.0.0.0') # This means "listen to all addresses on all interfaces"
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#options(DT.options = list(scrollX = TRUE))
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# An "application token" is required here. I generated this one like this:
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# curl -H "Content-Type: application/json" -d '{"name":"r-data"}' -u <username>:<password> https://git.tunstall.in/api/v1/users/sethp/tokens
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# Gitea access token
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access_token = read_lines("~/secret-token")
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gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/data_dashboard/list_unique_missense_genes.csv"
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missense_gene_url = "https://git.tunstall.in/api/v1/repos/tanu/fellowship_dcdf/raw/tb_data_fc/data_dashboard/missense_genes_params.csv"
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alphafold_url = "https://alphafold.ebi.ac.uk/files/"
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genes=read_csv(paste0(gene_url,"?token=",access_token))
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unique_missense_genes = read_delim(paste0(missense_gene_url,"?token=",access_token))
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44
server.R
44
server.R
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@ -83,11 +83,13 @@ shinyServer(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_pdb = as.character(unique_missense_genes[input$table_rows_selected,"position_pdb"])
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mutation_af = as.character(unique_missense_genes[input$table_rows_selected,"position_af"])
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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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#clicked_position = regmatches(mutation, regexpr("[0-9]+", mutation, perl=TRUE))
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# Now update the 3D structure to highlight the clicked thing and then zoom in.
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@ -96,7 +98,7 @@ shinyServer(function(input, output) {
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addSelection('spacefill'
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, param = list(
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name = "Pos"
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, sele = trimws(paste0(clicked_position,':', chain))
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, sele = trimws(paste0(mutation_pdb,':', chain))
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, color = "red"
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#, colorValue="00ff00"
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#, colorScheme="element"
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@ -107,7 +109,7 @@ shinyServer(function(input, output) {
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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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, sele = mutation_af
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, color = "red"
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#, colorValue="00ff00"
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#, colorScheme="element"
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@ -115,20 +117,20 @@ shinyServer(function(input, output) {
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)
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NGLVieweR_proxy("af_structure") %>% updateZoomMove(
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center = clicked_position,
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zoom = clicked_position,
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center = mutation_af,
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zoom = mutation_af,
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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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NGLVieweR_proxy("structure") %>% updateZoomMove(
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center = trimws(paste0(clicked_position,':', chain)),
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zoom = trimws(paste0(clicked_position,':', chain)),
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center = trimws(paste0(mutation_pdb,':', chain)),
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zoom = trimws(paste0(mutation_pdb,':', 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$table_rows_selected,"mutationinformation"]),"<br/>",
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HTML(paste0("<strong>Mutation: </strong>", as.character(unique_missense_genes[input$table_rows_selected,"mutationinformation_pdb"]),"<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$table_rows_selected,"ligand_distance"]), "<br/>",
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@ -186,7 +188,21 @@ shinyServer(function(input, output) {
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" and (",
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paste0(
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apply(
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unique_missense_genes[unique_missense_genes$gene_name == gene,c("position","chain")],
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unique_missense_genes[unique_missense_genes$gene_name == gene,c("position_pdb","chain")],
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1,
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function(x){
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paste0(trimws(x[1])
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)}
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),
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collapse=", "
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), ")"
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)
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mutations_af = paste0(":",
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as.matrix(unique_missense_genes[unique_missense_genes$gene_name == gene,c("chain")])[1],
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" and (",
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paste0(
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apply(
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unique_missense_genes[unique_missense_genes$gene_name == gene,c("position_af","chain")],
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1,
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function(x){
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paste0(trimws(x[1])
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@ -207,7 +223,7 @@ shinyServer(function(input, output) {
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opacity = 0.2
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)
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) %>%
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addSelection(type="ball+stick", #spacefill
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addSelection(type="spacefill", #spacefill
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param = list(name = "all_mutations",
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color="orange",
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sele = mutations
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@ -225,14 +241,14 @@ shinyServer(function(input, output) {
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opacity = 0.2
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)
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) %>%
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addSelection(type="ball+stick", #spacefill
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addSelection(type="spacefill", #spacefill
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param = list(name = "all_mutations",
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color="orange",
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sele = mutations
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sele = mutations_af
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#colorScheme = "bfactor",
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#opacity = 1
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)
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)
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})
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}
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)
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})
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1
ui.R
1
ui.R
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@ -12,7 +12,6 @@ library(NGLVieweR)
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library(httr)
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library(readr)
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library(RCurl)
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dashboardPage(skin="purple",
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dashboardHeader(title="Tuberculosis Host"),
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dashboardSidebar(
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