# no need to change directory. Just copy global.R, ui.R and server.R to 'demo-app' directry. direc = "/srv/shiny-server/" dataDirec= "/var/www/downloads/supplement_data/" dataDirec0 = "/var/www/downloads/" consDirec= "/var/www/downloads/coexp_cons/" .libPaths("/usr/local/lib/R/site-library") # Load in Rdata # load(paste0(dir,'www/attr.Rdata')) # known gene names and various IDs for each species # load(paste0(dir,'www/gotree.Rdata')) # Gene ontology tree (first few layers) # load("/ftp/data/gene2go/voc.Rdata") # descrptions of GO terms # load(paste0(dir,'www/goa.Rdata')) # gene x function binaries for each species # load(paste0(direc,'www/EGADlite.Rdata')) # load('www/GOlist.Rdata') # cc / bp / mf trees # enableBookmarking(store = "server") ##### config file ####### # /etc/shiny-server/shiny-server.conf ##### To install new packages ... # sudo su - -c "R -e \"install.packages('shiny', repos= 'http://cran.rstudio.com/' )\"" # repos='http://cran.rstudio.com/' ##### # (GRCh38) , (GRCm38) (TAIR10) (UMD3.1) (WBcel235) (GRCz11) (BDGP6) (Gallus_gallus-5.0) (Glycine_max_v2.0) (Rnor_6.0) (R64-1-1) (Sscrofa11.1) (rIRGSP-1.0) (maiAGPv4) speciesList = list( "Homo sapiens - Human" ='human', 'Mus musculus - Mouse' ='mouse', "Arabidopsis thaliana - Thale cress" ="arabidopsis", "Bos taurus - Cow" ="cow", "Caenorhabditis elegans - Roundworm" ="roundworm", "Danio rerio - Zebrafish" ="zebrafish", "Drosophila melanogaster - Fruitfly" ="fruitfly", "Gallus gallus - Chicken" ="chicken", "Glycine max - Soybean" ="soybean", "Rattus norvegicus - Rat" ="rat", "Saccharomyces cerevisiae - Budding yeast" ="yeast", "Sus scrofa - Pig" ="pig", "Oryza sativa - Rice" ="rice", "Zea mays - Maize" ="maize", "Salmo salar - Salmon" ='atlantic_salmon', 'Apis mellifera - Honey Bee' ='bee', 'Bombyx mori - Silkworm' ='silkworm', 'Brachypodium distachyon - Brome' ='brome', 'Pan troglodytes - Chimpanzee' ='chimp', 'Chlamydomonas reinhardtii - Chlamydomonas' ='chlamydomonas', 'Macaca fascicularis - Crab-eating macaque' ='crab_eating_macaque', 'Canis lupus familiaris - Dog' ='dog', # 'Schizosaccharomyces pombe - Fission yeast' ='fission_yeast', 'Capra hircus - Goat' ='goat', 'Vitis vinifera - Grape' ='grape', 'Equus caballus - Horse' ='horse', 'Medicago truncatula - Medicago' ='medicago', 'Aedes aegypti - Mosquito' ='aedes_aegypti', 'Solanum tuberosum - Potato' ='potato', 'Oryctolagus cuniculus - Rabbit' ='rabbit', 'Macaca mulatta - Rhesus macaque' ='rhesus_macaque', 'Ovis aries - Sheep' ='sheep', 'Sorghum bicolor - Sorghum' ='sorghum', 'Solanum lycopersicum - Tomato' ='tomato', 'Xenopus tropicalis - Western clawed frog' ='western_frog', # 'Xenopus tropicalis - African clawed frog' = 'african_frog', # 'Neurospora crassa - Neurospora' = 'neurospora', 'Brassica rapa - Mustard' = 'mustard', 'Malus domestica - Apple' = 'apple', 'Nicotiana tabacum - Tobacco' = 'tobacco', 'Oncorhynchus mykiss - Rainbow Trout' = 'rainbow_trout' ) # should sort by phylogeny - alphabetical for now speciesList=speciesList[c(1:2, 2+order(names(speciesList[3:length(speciesList)])))] speciesList2 = list( "Homo sapiens - Human" ='human', "Pan troglodytes - Chimpanzee" ='chimp', 'Macaca mulatta - Rhesus macaque' ='rhesus_macaque', 'Macaca fascicularis - Crab-eating macaque' ='crab_eating_macaque', 'Chlorocebus sabaeus - Green monkey' ='green_monkey', 'Callithrix jacchus - Marmoset' ='marmoset', 'Mus musculus - Mouse' ='mouse', "Rattus norvegicus - Rat" ="rat", 'Oryctolagus cuniculus - Rabbit' ='rabbit', "Sus scrofa - Pig" ="pig", 'Ovis aries - Sheep' ='sheep', 'Capra hircus - Goat' ='goat', "Bos taurus - Cow" ="cow", 'Equus caballus - Horse' ='horse', 'Canis lupus familiaris - Dog' ='dog', 'Felis catus - Cat' ='cat', "Gallus gallus - Chicken" ="chicken", 'Xenopus tropicalis - Western clawed frog' ='western_frog', 'Xenopus tropicalis - African clawed frog' = 'african_frog', "Danio rerio - Zebrafish" ="zebrafish", "Salmo salar - Salmon" ='atlantic_salmon', 'Oncorhynchus mykiss - Rainbow Trout' = 'rainbow_trout', "Caenorhabditis elegans - Roundworm" ="roundworm", 'Apis mellifera - Honey Bee' ='bee', 'Bombyx mori - Silkworm' ='silkworm', "Drosophila melanogaster - Fruitfly" ="fruitfly", 'Aedes aegypti - Mosquito' ='aedes_aegypti', "Saccharomyces cerevisiae - Budding yeast" ="yeast", 'Schizosaccharomyces pombe - Fission yeast' ='fission_yeast', 'Neurospora crassa - Neurospora' = 'neurospora', "Arabidopsis thaliana - Thale cress" ="arabidopsis", 'Brassica rapa - Mustard' = 'mustard', "Glycine max - Soybean" ="soybean", 'Medicago truncatula - Medicago' ='medicago', 'Solanum lycopersicum - Tomato' ='tomato', 'Solanum tuberosum - Potato' ='potato', 'Nicotiana tabacum - Tobacco' = 'tobacco', 'Malus domestica - Apple' = 'apple', 'Vitis vinifera - Grape' ='grape', "Zea mays - Maize" ="maize", 'Sorghum bicolor - Sorghum' ='sorghum', "Oryza sativa - Rice" ="rice", 'Brachypodium distachyon - Brome' ='brome', 'Chlamydomonas reinhardtii - Chlamydomonas' ='chlamydomonas' ) # speciesList[3:length(speciesList)] = speciesList[ind+2] # library(SingleCellExperiment) # library(tidyverse) # library(scattermore) library(visNetwork,quietly = T) # library(Matrix,quietly = T) # library(tools,quietly=T) # library(ggplot2,quietly=T) # library(taRifx,quietly=T) # library(dplyr,quietly=T) ### library(plotly,quietly=T) #* # library(GO.db,quietly=T) # library(data.table,quietly=T) library(shiny,quietly=T) library(shinyWidgets,quietly=T) library(shinydashboard,quietly=T) # library(shinyTree,quietly=T) library(shinydashboardPlus,quietly=T) library(shinyBS,quietly=T) # bootstrap library(shinyalert,quietly=T) # library(rhdf5,quietly=T) library(matrixStats,quietly=T) library(RColorBrewer) library(DT,quietly=T) # library(rARPACK) # library(sna) # library(shinythemes,quietly=T) # library(EGAD) # library(shinyEventLogger) library(igraph,quietly=T) library(Matrix,quietly = T) library(tools,quietly=T) library(ggplot2,quietly=T) # load('www/attr/gene_annotations_mouse.Rdata') # assign('mouse_attr',attr) # load('www/attr/gene_annotations_human.Rdata') # assign('human_attr',attr) # load('www/attr/gene_annotations_arabidopsis.Rdata') # assign('arabidopsis_attr',attr) # load('www/attr/gene_annotations_rat.Rdata') # assign('rat_attr',attr) # load('www/attr/gene_annotations_maize.Rdata') # assign('maize_attr',attr) # load('www/attr/gene_annotations_chicken.Rdata') # assign('chicken_attr',attr) # load('www/attr/gene_annotations_fruitfly.Rdata') # assign('fruitfly_attr',attr) # load('www/attr/gene_annotations_soybean.Rdata') # assign('soybean_attr',attr) # load('www/attr/gene_annotations_cow.Rdata') # assign('cow_attr',attr) # load('www/attr/gene_annotations_yeast.Rdata') # assign('yeast_attr',attr) # load('www/attr/gene_annotations_boar.Rdata') # assign('boar_attr',attr) # load('www/attr/gene_annotations_roundworm.Rdata') # assign('roundworm_attr',attr) # load('www/attr/gene_annotations_rice.Rdata') # assign('rice_attr',attr) # load('www/attr/gene_annotations_zebrafish.Rdata') # assign('zebrafish_attr',attr) # rm(attr) # Location of network data # loc = 'www/rankNormVals/' ########################## summary table for download data tab ############################## ########################## Graph, description box footer and static slider ############################## # tabPanel("Result3",icon = icon("bezier-curve"), # boxPlus(title = "boxPlus with footer and static slider",width = '',height='470px',status = "success", # closable=F,collapsible = T,footer_padding = F, # fluidRow(column(width=9,plotOutput('tab3plot')), # column(width=3, # checkboxInput("somevalue2", "Apply some condition", FALSE), # verbatimTextOutput("value2"), # sliderInput("tab3slider","Number of observations:",min = 0,max = 1000,value = 200), # actionButton('tab3SliderButton','Update changes',icon=icon('magic'),width='auto') # )), # footer = fluidRow( # column(width=3, # descriptionBlock( # number = "17%", # number_color = "green", # number_icon = "fa fa-caret-up", # header = "header1", # text = "text1")), # column(width=3, # descriptionBlock( # number = "18%", # number_color = "yellow", # number_icon = "fa fa-caret-down", # header = "header4", # text = "text4", # right_border = F)) # ) # ) # ) ########################## Graph, description box and dynamic slider ############################## # tabPanel("Result1",icon = icon("chart-bar"), # boxPlus(title = "boxPlus with dynamic sidebar",width='',height='520px',status = "warning", # collapsible = T,closable = T,enable_sidebar = TRUE,sidebar_width = 25, # sidebar_start_open = T,footer_padding = F,sidebar_background = "#001F3F", # sidebar_content = tagList( # checkboxInput("somevalue", "Apply some condition", FALSE), # verbatimTextOutput("value"), # sliderInput("slider_boxsidebar","Number of observations:", # min = 0,max = 1000,value = 700), # actionButton('tab1SliderButton','Update changes',icon=icon('magic'),width='auto') # ), # plotOutput("boxSidebarPlot",width='auto',height='480px'))), ####################################### Gradient Box #################################################### # boxPlus(title = "boxPlus with gradient box and boxPad",width = '',height='520px',status = "danger", # closable=F,collapsible = T,footer_padding = T, # fluidRow(column(width=9, # gradientBox(plotOutput('tab2plot',height='300px'), # title='Gradient box with boxPad',icon=icon('heart'), # gradientColor='red',boxToolSize='xs',closable=T, # width=12,height='450px',collapsible =T,footer_padding=F, # footer=sliderInput("slider_gradient","Number of observations:", # min = 0,max = 1000,value = 700))), # column(width=3,height='480px', # boxPad(color = "green", height='480px', # descriptionBlock(header = "8390",text = "VISITS",right_border = F), # descriptionBlock(header = "30%",text = "REFERRALS",right_border = F), # descriptionBlock(header = "70%",text = "ORGANIC",right_border = F) # ) # )) # ) #######################################Different Tab views####################################### # #tabItem(tabName = "ortho", # navbarPage(title = "1-1 Ortholog Finder", # tabPanel('Input', # verticalLayout( # selectInput(inputId="species",label=h3("Select species:"),choices=geneList,selected=NULL), # selectInput(inputId="userGenes",label=h3("Select genes:"),multiple = T,choices=speciesList,selected=NULL), # textInput("geneList", h3("Enter gene"),value = "",placeholder ="Multiple genes should be separated by ','"), # fileInput("geneFile", h3("Upload gene list"), buttonLabel = 'Upload'), # actionButton("action", "Generate Results",icon('cogs')) # ) # ), # tabPanel("Result1",value='tab1',icon=icon("chart-bar"),"Result 1 displayed here..."), # tabPanel("Result2",value='tab2',icon=icon("hubspot"),"Result 2 displayed here..."), # tabPanel("Result3",value='tab3',icon=icon("bezier-curve"),"Result 3 displayed here...") # ) # ) # # # net3 # tabItem(tabName = "net3", # fluidPage( # titlePanel("Co-expression network generator"), # fillRow(flex=2, # verticalLayout( # selectInput(inputId="species",label=h3("Select species:"),choices=speciesList,selected=NULL), # selectInput(inputId="userGenes",label=h3("Select genes:"),multiple = T,choices=geneList,selected=NULL), # textInput("geneList", h3("Enter gene"), # value = "", # placeholder ="Multiple genes should be separated by ','"), # fileInput("geneFile", h3("Upload gene list"), buttonLabel = 'Upload'), # actionButton("action", "Generate Results",icon('cogs'))), # tabsetPanel( # #side = "left", height = "450px",id = 'netTabResult', # #selected = "Result1", width = '', # tabPanel("Result1",icon = icon("chart-bar"),"Result 1 displayed here..."), # tabPanel("Result2",icon = icon("hubspot"),"Result 2 displayed here..."), # tabPanel("Result3",icon = icon("bezier-curve"),"Result 3 displayed here...") # ) # ) # ) # ), ################################----individual histogram functions------################################################ ################################----GO group nestedlist generator----####################################### # treeGenerator <- function(children,ori){ # for(i in seq(length(children))){ # child = children[[i]] # if(!is.null(ori[[child]])){ # children[[child]] = treeGenerator(ori[[child]],ori)}} # return(children) # } # # lister <- function(vec){ # for(i in seq(length(vec))){ # vec[[i]]=sapply(as.vector(vec[[i]]),function(x) list(x))} # return(vec) # } # # cc <- as.list(GOCCCHILDREN) # cc <- cc[!is.na(cc)] # cc <- lister(cc) # cc_list = treeGenerator(cc[['GO:0005575']],cc) # bp <- as.list(GOBPCHILDREN) # bp <- bp[!is.na(bp)] # bp <- lister(bp) # bp_list = treeGenerator(bp[['GO:0008150']],bp) # mf <- as.list(GOMFCHILDREN) # mf <- mf[!is.na(mf)] # mf <- lister(mf) # mf_list = treeGenerator(mf[['GO:0003674']],mf) # b1 = list() # for(i in seq(nrow(res5))[-c(144,153:154)]){ # #a = res5[i,][!is.na(res5[i,])] # a = z[i,][!is.na(z[i,])] # print(i) # switch (length(a), # '1' = {b1[[a[1]]]=list()}, # '2' = { # if(is.null(b1[[a[1]]])){ # b1[[a[1]]]=list() # b1[[a[1]]][[a[2]]] = a[2] # } else { # b1[[a[1]]][[a[2]]] = a[2] # } # }, # '3' = { # if(is.null(b1[[a[1]]])){ # b1[[a[1]]]=list() # b1[[a[1]]][[a[2]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]] = a[3] # } else if(is.null(b1[[a[1]]][[a[2]]])) { # b1[[a[1]]][[a[2]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]] = a[3] # } else { # b1[[a[1]]][[a[2]]][[a[3]]] = a[3] # } # }, # '4' = { # if(is.null(b1[[a[1]]])){ # b1[[a[1]]]=list() # b1[[a[1]]][[a[2]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]][[a[4]]] = a[4] # } else if(is.null(b1[[a[1]]][[a[2]]])) { # b1[[a[1]]][[a[2]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]][[a[4]]] = a[4] # } else if(is.null(b1[[a[1]]][[a[2]]][[a[3]]])) { # b1[[a[1]]][[a[2]]][[a[3]]] = list() # b1[[a[1]]][[a[2]]][[a[3]]][[a[4]]] = a[4] # } else { # b1[[a[1]]][[a[2]]][[a[3]]][[a[4]]] = a[4] # } # }) # }