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app.R
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app.R
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library(shiny)
library(shinyjs)
library(tidyverse)
library(rlang)
library(DT)
library(shinycssloaders)
library(profvis)
result <- read_tsv("result.tsv") %>% mutate_if(is.integer, funs(as.double(.)))
chembl <- read_tsv("chembl.tsv", trim_ws = F)
drugb <- read_tsv("drugb.tsv", na = "NA")
ipro <- read_tsv("ipro.tsv", col_types = "cccn", na = "NA")
prot_types <- read_tsv("prot_types.tsv")
screenS <- read_tsv("screenS.tsv")
shdf <- read_tsv("shdf.tsv")
numprot <- shdf %>% select(MS3_id) %>% count() %>% pull()
wght <- rep(1, ncol(shdf)+2)
names(wght) <- c(colnames(shdf), "one_cmpd", "more_cmpds")
more_cmpds <- 5
ptdd <- c("All identifiers",paste(prot_types$ipro_id, prot_types$ipro_descr, sep = " "))
equalWeight <- 5
#set preselected cut-offs for blast coverage and similarity to determine homology
simil_cutoff <- 80
cov_cutoff <- 50
cutOff <- function(df, cut=0)
{
if_else(df >= cut, 1, 0)
}
# Define UI for Shiny app ----
ui <- tagList(useShinyjs(),
div(id = "navbar", navbarPage(title = "S. haematobium drug target ranking",
selected = "Transcription",
tabPanel("Transcription",
{
fluidRow(
column(5,
sliderInput(inputId = "trAdS", "Transcribed in adults?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "trAdRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "require", inline = T)
)
)
}
),
tabPanel("Orthology",
{
list(
fluidRow(
column(12,
numericInput(inputId = "sim_cut", label = "Similarity cut-off (%)", value = simil_cutoff, min = 0, max = 100),
numericInput(inputId = "cov_cut", label = "Coverage cut-off (%)", value = cov_cutoff, min = 0, max = 100)
)
),
fluidRow(
column(3,
sliderInput(inputId = "HomCelS", "Ortholog in C. elegans?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "HomCelRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "HomDmelS", "Ortholog in D. melanogaster?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "HomDmelRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "HomMusS", "Ortholog in M. musculus?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "HomMusRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "exclude", inline = T)
),
column(3,
sliderInput(inputId = "HomSjS", "Ortholog in S. japonicum?",
min = 1, max = 10, width = "100%",
value = 7, step = 1),
radioButtons(inputId = "HomSjRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "HomSmS", "Ortholog in S. mansoni?",
min = 1, max = 10, width = "100%",
value = 8, step = 1),
radioButtons(inputId = "HomSmRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T)
),
column(3,
sliderInput(inputId = "HomCsinS", "Ortholog in C. sinensis?",
min = 1, max = 10, width = "100%",
value = 6, step = 1),
radioButtons(inputId = "HomCsinRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "HomOvivS", label = "Ortholog in O. viverrini?",
min = 1, max = 10, width = "100%",
value = 6, step = 1),
radioButtons(inputId = "HomOvivRB", label = "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "HomFhepS", label = "Ortholog in F. hepatica?",
min = 1, max = 10, width = "100%",
value = 8, step = 1),
radioButtons(inputId = "HomFhepRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T)
),
column(3,
sliderInput(inputId = "HomSPS", "Ortholog in SwissProt?",
min = 1, max = 10, width = "100%",
value = 7, step = 1),
radioButtons(inputId = "HomSPRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "quant_slider", "No ortholog or similarity <75th percentile of H. sapiens?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "QuantHsRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "require", inline = T)
)
)
)
}
),
tabPanel("Essentiality",
{ fluidRow(
column(6,
sliderInput(inputId = "letCelS", "Lethal phenotype C. elegans?",
min = 1, max = 10, width = "100%",
value = 9, step = 1),
radioButtons(inputId = "letCelRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "letDmelS", "Lethal phenotype D. melanogaster?",
min = 1, max = 10, width = "100%",
value = 9, step = 1),
radioButtons(inputId = "letDmelRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "letMusS", "Lethal phenotype M. musculus?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "letMusRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "exclude", inline = T
)
),
column(6,
sliderInput(inputId = "chokeS", "Unique KEGG term ('choke-point')?",
min = 1, max = 10, width = "100%",
value = 8, step = 1),
radioButtons(inputId = "chokeRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"),selected = "weighted", inline = T),
sliderInput(inputId = "uniqIproS", "Unique InterPro identifier?",
min = 1, max = 10, width = "100%",
value = 7, step = 1),
radioButtons(inputId = "uniqIproRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T)
)
)
}
),
tabPanel("Annotation",
{
fluidRow(
column(12,
selectInput("prot_type", label = "Select InterPro protein identifier(s)", selected = ptdd[1], choices = ptdd, multiple = T, width = '100%'),
radioButtons(inputId = "groupcheck", "", choices = c("ANY OF SELECTED" = "requireAny", "ALL OF SELECTED" = "requireAll", "NONE OF SELECTED" = "exclude"), selected = "requireAny", inline = T)
)
)
}
),
tabPanel("Drugs",
{
fluidRow(
column(6,
h2("ChEMBL"),
sliderInput(inputId = "ChCmpdOneS", "At least one associated compound in ChEMBL?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "ChCmpdOneRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "require", inline = T),
sliderInput(inputId = "ChCmpdMoreS", paste(more_cmpds, " or more associated compounds in ChEMBL?"),
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "ChCmpdMoreRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
sliderInput(inputId = "chPhase", "Drug phase",
min = 0, max = 4, width = "100%",
value = c(2,4), step = 1),
sliderInput(inputId = "Ch_ro5_viol", "Max. no. of rule-of-5 violations",
min = 0, max = 3, width = "100%",
value = 0, step = 1),
h5("Other requirements"),
checkboxInput(inputId = "Ch_ro3_pass", label = "Require rule-of-3 pass"),
checkboxInput(inputId = "InNatProd", label = "Require compounds to be natural products"),
checkboxInput(inputId = "InScreenedSchisto", label = "Require drug screening data for schistosomes", value = TRUE)
),
column(6,
h2("DrugBank"),
sliderInput(inputId = "DBCmpdOneS", "At least one associated compound in DrugBank?",
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "DBCmpdOneRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "require", inline = T),
sliderInput(inputId = "DBCmpdMoreS", paste(more_cmpds, " or more associated compounds in DrugBank?"),
min = 1, max = 10, width = "100%",
value = equalWeight, step = 1),
radioButtons(inputId = "DBCmpdMoreRB", "",
c("WEIGHTED" = "weighted",
"IGNORE" = "ignore",
"REQUIRE" = "require",
"EXCLUDE" = "exclude"), selected = "weighted", inline = T),
checkboxGroupInput(inputId = "DBstatus",
choiceValues = c("approved",
"experimental",
"illicit",
"investigational",
"nutraceutical",
"withdrawn"),
choiceNames = c("Approved",
"Experimental",
"Illicit",
"Investigational",
"Nutraceutical",
"Withdrawn"),
selected = "approved", label = "Include drugs with status/properties"
),
h5("Other requirements"),
checkboxInput(inputId = "InMDDR", label = "Require MDDR-likeness"),
checkboxInput(inputId = "InRo5", label = "Require rule-of-5 pass", value = TRUE)
)
)
}
),
tabPanel("Summary and Analysis",
{
list(
fluidRow(
column(4,
actionButton("reset_input", "Reset weights"),
actionButton("calc", "Calculate ranking"),
tableOutput(outputId = "outTable")
),
column(8,
textOutput(outputId = "numRes"),
plotOutput(outputId = "scoredistr") %>% withSpinner(),
uiOutput("downloads"),
uiOutput(outputId = "DBversions")
#,
#dataTableOutput(outputId = "drugSelTable")
)
),
fluidRow(
column(12,
dataTableOutput(outputId = "protSelTable") %>% withSpinner()
)
)
)
}
)
,
navbarMenu("Drug Results",
tabPanel("ChEMBL",
fluidRow(
column(12,
uiOutput("CHout"),
uiOutput("CHdl"),
dataTableOutput(outputId = "drugSelTableCH") %>% withSpinner()
)
)
),
tabPanel("DrugBank",
fluidRow(
column(12,
uiOutput("DBout"),
uiOutput("DBdl"),
dataTableOutput(outputId = "drugSelTableDB") %>% withSpinner()
)
)
)
)
)
)
)
# Define server side ----
server <- function(input, output, session) {
#Gather data for selected proteins
gatherProtSelect <- eventReactive(eventExpr = input$calc,
{
if("All identifiers" %in% input$prot_type)
{
selectProt <- c("",ptdd[-1])
}
else
{
selectProt <- as.vector(input$prot_type)
}
#Get just the IDs (minus the actual description) of the selected protein identifiers
selectProt <- str_sub(selectProt, 1,9)
if(input$groupcheck == "requireAny")
{
id_tbl <- ipro %>%
filter(ipro_id %in% selectProt) %>%
select(MS3_id) %>%
distinct()
}
else
{
if(input$groupcheck == "requireAll")
{
#this statement returns MS3_id
#find all MS3_id that have a row for all of the values in selectProt
id_tbl <- ipro %>%
group_by(MS3_id) %>%
filter(., all(selectProt %in% ipro_id)) %>%
select(MS3_id) %>%
distinct() %>% ungroup()
}
else
{
if(input$groupcheck == "exclude")
{
id_tbl <- ipro %>%
filter(ipro_id %in% selectProt) %>%
select(MS3_id) %>%
distinct() %>%
anti_join(ipro, ., by = "MS3_id") %>%
select(MS3_id) %>%
distinct()
}
}
}
#subset the result based on the selection made by the user
subsResult <- inner_join(id_tbl, result, by="MS3_id") %>%
mutate_at(vars(ends_with("_simil")), funs(replace_na(., 0))) %>%
mutate_at(vars(ends_with("_cov")), funs(replace_na(., 0))) %>%
#if the cov or simil value in the result table is bigger than the selected cut-off, set it to 1
# else set it to 0
mutate_at(vars(ends_with("_simil")), funs(cutOff(., cut = input$sim_cut))) %>%
mutate_at(vars(ends_with("_cov")), funs(cutOff(., cut = input$cov_cut/100))) %>%
gather(type, value, union(ends_with("_simil"), ends_with("_cov"))) %>%
separate(type, into = c("Species", "simCov")) %>%
arrange(MS3_id, Species, simCov) %>%
group_by(MS3_id, Species) %>%
mutate(value = max(value)) %>%
ungroup %>%
filter(simCov == "cov") %>%
unite(Species, simCov, col = "column1", sep = "_") %>%
spread(column1, value) %>%
select(MS3_id,
male_tpm,
cel_leth,
dmel_leth,
mus_leth,
chokepoint,
uniqIpro,
cel_cov,
dmel_cov,
mus_cov,
sjap_cov,
sman_cov,
closi_cov,
opvi_cov,
fahe_cov,
sp_cov,
hsa_lower_75_qtl,
ChCmpdOne,
ChCmpdMore,
DBCmpdOne,
DBCmpdMore
)
tibOut <- tibble(
name = c(
"male_tpm",
"cel_leth",
"dmel_leth",
"mus_leth",
"chokepoint",
"uniqIpro",
"cel_cov",
"dmel_cov",
"mus_cov",
"sjap_cov",
"sman_cov",
"closi_cov",
"opvi_cov",
"fahe_cov",
"sp_cov",
"hsa_lower_75_qtl",
"ChCmpdOne",
"ChCmpdMore",
"DBCmpdOne",
"DBCmpdMore"
),
weighted = c(
input$trAdS,
input$letCelS,
input$letDmelS,
input$letMusS,
input$chokeS,
input$uniqIproS,
input$HomCelS,
input$HomDmelS,
input$HomMusS,
input$HomSjS,
input$HomSmS,
input$HomCsinS,
input$HomOvivS,
input$HomFhepS,
input$HomSPS,
input$quant_slider,
input$ChCmpdOneS,
input$ChCmpdMoreS,
input$DBCmpdOneS,
input$DBCmpdMoreS
),
mode = as.character(c(
input$trAdRB,
input$letCelRB,
input$letDmelRB,
input$letMusRB,
input$chokeRB,
input$uniqIproRB,
input$HomCelRB,
input$HomDmelRB,
input$HomMusRB,
input$HomSjRB,
input$HomSmRB,
input$HomCsinRB,
input$HomOvivRB,
input$HomFhepRB,
input$HomSPRB,
input$QuantHsRB,
input$ChCmpdOneRB,
input$ChCmpdMoreRB,
input$DBCmpdOneRB,
input$DBCmpdMoreRB
))
)
newWeights <- filter(tibOut ,mode == "weighted") %>% select(., name, weighted) %>% spread(.,name,weighted)
if(!is_empty(newWeights)){
for (nm in names(newWeights)) {
subsResult[nm] <- subsResult[nm]*as.double(newWeights[1,nm])
}
}
required <- select(tibOut, name, mode) %>% filter(.,mode == "require") %>% pull(., var="name")
if(!is_empty(required)){
subsResult <- filter_at(subsResult, vars(required), all_vars(. > 0))
subsResult <- select(subsResult, -(one_of(required)))
}
excluded <- select(tibOut, name, mode) %>% filter(.,mode == "exclude") %>% pull(., var="name")
if(!is_empty(excluded)){
subsResult <- filter_at(subsResult, vars(excluded), all_vars(. == 0))
subsResult <- select(subsResult, -(one_of(excluded)))
}
ignored <- select(tibOut, name, mode) %>% filter(.,mode == "ignore") %>% pull(., var="name")
if(!is_empty(ignored)){
subsResult <- select(subsResult, -(one_of(ignored)))
}
subsResult <- mutate(subsResult, score = rowSums(subsResult[,-1])) %>% arrange(.,desc(score))
plotout <- ggplot(subsResult, aes(score)) + geom_bar(fill = "seagreen4") + labs(x = "Score", y = "Frequency") + theme_minimal() + theme(text = element_text(size = 16))
NonDistRes <- as.character(subsResult %>% select(MS3_id) %>% count())
list(table = subsResult, plot = plotout, text = paste(NonDistRes, sep = ""))
}
)
# Define output server side ----
# Create table of selected parameters as an output on the UI
output$outTable <- renderTable(
makeParamsTable()
)
# Create table of selected parameters
makeParamsTable <- reactive(
{
outtbl <- tibble(
Criterion = c(
#"male_tpm",
"Transcribed in adults?",
#"cel_leth",
"Lethal phenotype in C. elegans?",
#"dmel_leth",
"Lethal phenotype in D. melanogaster?",
#"mus_leth",
"Lethal phenotype in M. musculus?",
#"chokepoint",
"KEGG 'choke-point'?",
#"uniqIpro",
"Unique InterPro identifier?",
#"cel_cov",
"C. elegans ortholog?",
#"dmel_cov",
"D. melanogaster ortholog?",
#"mus_cov",
"M. musculus ortholog?",
#"sjap_cov",
"S. japonicum ortholog?",
#"sman_cov",
"S. mansoni ortholog?",
#"closi_cov",
"C. sinensis ortholog?",
#"opvi_cov",
"O. viverrini ortholog?",
#"fahe_cov",
"F. hepatica ortholog?",
#"sp_cov",
"SwissProt ortholog?",
#"hsa_lower_75_qtl",
"Similarity to H. sapiens ortholog <75th percentile?",
#"ChCmpdOne",
"At least one associated compound in ChEMBL",
#"ChCmpdMore",
paste(more_cmpds, " or more associated compounds in ChEMBL?"),
#"DBCmpdOne",
"At least one associated compound in DrugBank",
#"DBCmpdMore"
paste(more_cmpds, " or more associated compounds in DrugBank?")
),
Weight = c(
input$trAdS,
input$letCelS,
input$letDmelS,
input$letMusS,
input$chokeS,
input$uniqIproS,
input$HomCelS,
input$HomDmelS,
input$HomMusS,
input$HomSjS,
input$HomSmS,
input$HomCsinS,
input$HomOvivS,
input$HomFhepS,
input$HomSPS,
input$quant_slider,
input$ChCmpdOneS,
input$ChCmpdMoreS,
input$DBCmpdOneS,
input$DBCmpdMoreS
),
"Ranking mode" = factor(c(
input$trAdRB,
input$letCelRB,
input$letDmelRB,
input$letMusRB,
input$chokeRB,
input$uniqIproRB,
input$HomCelRB,
input$HomDmelRB,
input$HomMusRB,
input$HomSjRB,
input$HomSmRB,
input$HomCsinRB,
input$HomOvivRB,
input$HomFhepRB,
input$HomSPRB,
input$QuantHsRB,
input$ChCmpdOneRB,
input$ChCmpdMoreRB,
input$DBCmpdOneRB,
input$DBCmpdMoreRB
))
)
arrange(outtbl, UQ(sym("Ranking mode")))
}
)
# Summary sentence of how many proteins were found that match the user criteria
output$numRes <- renderText(
{
out <- gatherProtSelect()
paste("Of ", numprot, " proteins, ", unlist(out$text), " match your protein filtering criteria, with the following score distribution:")
}
)
# Summary sentence of how many proteins were found that match the user criteria
output$DBversions <- renderUI(
{
out <- gatherProtSelect()
HTML(paste(
"",
"Results are calculated using the following database versions/releases:",
"WormBase: WS262",
"FlyBase: FB2017_06",
"Ensembl: 91.38",
"WormBase Parasite: WBPS9",
"Swiss-Prot: 05/2017",
"KEGG: 05/2017",
"InterProScan: 5.15.54",
"ChEMBL: 23",
"DrugBank: 5-0-11",
sep="<br/>"))
}
)
# Make plot of the score distribution
output$scoredistr <- renderPlot(
{
out <- gatherProtSelect()
out$plot
}
)
# Clean up and create a table for viewing on UI
createTable <- reactive(
{
out <- gatherProtSelect()
out$table <- out$table %>%
select(MS3_id) %>%
left_join(., ipro) %>%
select(MS3_id, ipro_descr) %>%
distinct() %>%
group_by(MS3_id) %>%
summarise(anno = paste0(ipro_descr, collapse = "; ")) %>%
ungroup() %>%
select(MS3_id, anno) %>%
right_join(., out$table, by = "MS3_id") %>%
left_join(., select(shdf, MS3_id, gene_name_species, uniprot_id), by = "MS3_id") %>%
mutate(gene_name_species = paste(gene_name_species, uniprot_id, sep = " ")) %>%
mutate_at(., vars(gene_name_species), funs(if_else(. == "NA NA", "", .))) %>%
select(-uniprot_id) %>%
select(
MS3_id,
score,
anno,
gene_name_species,
everything()
)
}
)
# Create two different drug tables on click
DrugCHTable <- eventReactive(eventExpr = input$show_drug_chembl,
{
tab <- createTable() %>% slice(1:isolate(input$num_dl_chembl)) %>%
select(MS3_id) %>%
left_join(., chembl) %>%
select(
MS3_id,
acc_no,
chembl_target_id,
ro5_viol,
ro3_pass,
target_name,
cmpd_name,
cmpd_syn,
chembl_cmpd_id,
smiles,
phase,
nat_prod,
first_approv,
pat_no,
pat_exp
)
tab <- tab %>% select(-c(cmpd_name, cmpd_syn, pat_no, pat_exp)) %>% distinct() %>%
left_join(.,
{
tab %>% select(chembl_cmpd_id, cmpd_name, cmpd_syn, pat_no, pat_exp) %>%
distinct() %>%
mutate(cmpd_name = str_to_title(cmpd_name)) %>%
mutate(cmpd_syn = str_to_title(cmpd_syn)) %>%
group_by(chembl_cmpd_id) %>%
mutate(cmpd_name = paste0(unique(cmpd_name), collapse = "; ")) %>% distinct() %>%
mutate(cmpd_syn = paste0(unique(cmpd_syn), collapse = "; ")) %>% distinct() %>%
mutate(pat_no = str_replace(pat_no, "^None$" , NA_character_)) %>%
mutate(pat_exp = str_replace(pat_exp, "^None$" , NA_character_)) %>%
mutate(pat_no = paste(pat_no[!is.na(pat_no)], " (exp. ", pat_exp[!is.na(pat_exp)], ")", sep = "", collapse = "; ")) %>%
ungroup() %>% select(-pat_exp) %>% distinct() %>%
mutate(pat_no = str_replace(pat_no, "[:blank:]\\(exp\\.[:blank:]\\)" , "")) %>%
mutate(cmpd_name = str_replace(cmpd_name, "^NA$" , "")) %>%
mutate(cmpd_syn = str_replace(cmpd_syn, "^NA$" , ""))
}
, by = "chembl_cmpd_id"
) %>%
select(
MS3_id,
acc_no,
chembl_target_id,
ro5_viol,
ro3_pass,
target_name,
cmpd_name,
cmpd_syn,
chembl_cmpd_id,
smiles,
phase,
nat_prod,
first_approv,
pat_no
)
tab <- tab %>% filter(ro5_viol <= input$Ch_ro5_viol | is.na(ro5_viol)) %>%
filter(phase %in% range(input$chPhase) | is.na(phase))
if(input$Ch_ro3_pass){
tab <- tab %>% filter(ro3_pass == "Y")
}
if(input$InNatProd){
tab <- tab %>% filter(nat_prod == "yes")
}
if(input$InScreenedSchisto){
tab <- tab %>% filter(chembl_cmpd_id %in% screenS$chembl_cmpd_id)
}
tab <- tab %>% left_join(screenS, by = "chembl_cmpd_id")
tab
}
)
DrugDBTable <- eventReactive(eventExpr = input$show_drug_db,
{
tab <- createTable() %>%
slice(1:isolate(input$num_dl_db)) %>%
select(MS3_id) %>%
left_join(., drugb)
tab <- tab %>% filter(status %in% input$DBstatus | is.na(status))
if(input$InMDDR){
tab <- tab %>% filter(mddr.like == 1)
}
if(input$InRo5){
tab <- tab %>% filter(ro5_pass == 1)
}
tab <- tab %>%
mutate_at(.,
vars(ro5_pass, mddr.like),
funs(
if_else(. == 1, "yes", "no")
)
)
tab
}
)
# Create link for drug IDs to add to data table
createLinkCH <- function(val) {
sprintf('<a href="https://www.ebi.ac.uk/chembl/compound/inspect/%s" target="_blank" class="btn btn-primary">%s</a>',val, val)
}
createLinkDB <- function(val) {
sprintf('<a href="https://www.drugbank.ca/drugs/%s" target="_blank" class="btn btn-primary">%s</a>',val, val)
}
# Create datatables for drug output
output$drugSelTableCH <- renderDataTable(
{
tableCH <- DrugCHTable()
tableCH$chembl_cmpd_id <- createLinkCH(tableCH$chembl_cmpd_id)
tableCH$chembl_cmpd_id[tableCH$chembl_cmpd_id == '<a href=\"https://www.ebi.ac.uk/chembl/compound/inspect/NA\" target=\"_blank\" class=\"btn btn-primary\">NA</a>'] <- ""
columns <- tibble(name = colnames(tableCH))
lookup <- as.tibble(matrix(
c(
"MS3_id", "Identifier",
"acc_no", "Target accession number",
"chembl_target_id", "Target ID",
#"target_type", "Target type",
"ro5_viol", "Ro5 violations",
"ro3_pass", "Ro3 pass",
"target_name", "Target name",
"cmpd_name", "Compound name(s)",
"cmpd_syn", "Compound synonym(s)",
"chembl_cmpd_id", "Compound ID",
"smiles", "SMILES",
"phase", "Drug phase",
"nat_prod", "Natural product?",
"first_approv", "Approval date",
"pat_no", "Patent number(s) (expiry date)",
"link", "Screening data for Schistosoma"
),
ncol = 2, byrow = T
)
)
colnames(lookup) <- c("name", "cleanname")
cleannames <- columns %>% left_join(., lookup, by = "name") %>% select(cleanname) %>% pull()
datatable(
data = tableCH
, colnames = cleannames
, options = list(scrollX = T, lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')))
, escape = F
)
}
)
output$drugSelTableDB <- renderDataTable(
{
tableDB <- DrugDBTable()
columns <- tibble(name = colnames(tableDB))
tableDB$cmpd_id <- createLinkDB(tableDB$cmpd_id)
tableDB$cmpd_id[tableDB$cmpd_id == '<a href=\"https://www.drugbank.ca/drugs/NA\" target=\"_blank\" class=\"btn btn-primary\">NA</a>'] <- ""