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Shiny_MotifX_051023.R
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Shiny_MotifX_051023.R
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run_motifx <- function(input, output, data_in){
cat(file=stderr(), "start motifx..." , "\n")
require(stringr)
require(stringi)
require(PTMphinder)
require(rmotifx)
#---------Create background data ----------------------------------------
# Set parameters for extractBackground (s - sequence list; c - central character; w - width of motifs
parsed_ref <- dpmsr_set$data$phos$background
s <- parsed_ref$Sequence
w <- 15
pval_motif <- input$pval_motif * 1e-5
min_seq <- as.integer(input$motif_min_seq)
parsed_refx <<- parsed_ref
sx <<- s
wx <<- w
pval_motifx <<- pval_motif
data_inx <<- data_in
pvalue_cutoffx <<- input$pvalue_cutoff
foldchange_cutoffx <<- input$foldchange_cutoff
select_data_comp_motifx <<- input$select_data_comp_motif
cat(file=stderr(), "motifx up..." , "\n")
filter_df <- subset(data_in, data_in$Stats == "Up" )
if (nrow(filter_df > 0)){
FC <- "Up"
ptm_data <- create_motifx_input(filter_df, parsed_ref, input$select_data_comp_motif, "Up")
cat(file=stderr(), str_c("ptm_data has ", nrow(ptm_data), " entries") , "\n")
motifx_S <- motifx_calc(s, "S", w, "Up", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
cat(file=stderr(), str_c("motifx_S has ", nrow(motifx_S), " entries") , "\n")
motifx_T <- motifx_calc(s, "T", w, "Up", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
cat(file=stderr(), str_c("motifx_T has ", nrow(motifx_T), " entries") , "\n")
motifx_Y <- motifx_calc(s, "Y", w, "Up", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
cat(file=stderr(), str_c("motifx_Y has ", nrow(motifx_Y), " entries") , "\n")
motifx_up <- rbind(motifx_S, motifx_T, motifx_Y)
cat(file=stderr(), str_c("motifx_up has ", nrow(motifx_up), " entries") , "\n")
}else{
motifx_up <- NULL
shinyalert("Oops!", "No peptides passed stats for Up", type = "error")
}
cat(file=stderr(), "motifx down..." , "\n")
filter_df <- subset(data_in, data_in$Stats == "Down" )
if (nrow(filter_df > 0)){
FC <<- "Down"
ptm_data <- create_motifx_input(filter_df, parsed_ref, input$select_data_comp_motif, "Down")
motifx_S <- motifx_calc(s, "S", w, "Down", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
motifx_T <- motifx_calc(s, "T", w, "Down", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
motifx_Y <- motifx_calc(s, "Y", w, "Down", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
motifx_down <- rbind(motifx_S, motifx_T, motifx_Y)
}else{
motifx_down <- NULL
shinyalert("Oops!", "No peptides passed stats for Down", type = "error")
}
cat(file=stderr(), "motifx updown..." , "\n")
filter_df<- subset(data_in, data_in$Stats == "Up" | data_in$Stats == "Down")
if (nrow(filter_df > 0)){
FC <- "UpDown"
ptm_data <- create_motifx_input(filter_df, parsed_ref, input$select_data_comp_motif, "UpDown")
motifx_S <- motifx_calc(s, "S", w, "UpDown", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
motifx_T <- motifx_calc(s, "T", w, "UpDown", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
motifx_Y <- motifx_calc(s, "Y", w, "UpDown", ptm_data, parsed_ref, pval_motif, min_seq, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
motifx_updown <- rbind(motifx_S, motifx_T, motifx_Y)
}else{
motifx_updown <- NULL
shinyalert("Oops!", "No peptides passed stats for UpDown", type = "error")
}
cat(file=stderr(), str_c("compiling motifs... ", nrow(motifx_up), "... ", nrow(motifx_down), "... ", nrow(motifx_updown)) , "\n")
motifx_all <- rbind(motifx_up, motifx_down, motifx_updown)
if(is.null(motifx_all)){
shinyalert("Oops!", "No motifx found", type = "error")
}else {
cat(file=stderr(), "write motifx excel..." , "\n")
# save filename to dpmsr_set so downloadhandler can grab it
dpmsr_set$data$phos$filename <<- str_c("MotifX_", input$select_data_comp_motif, ".xlsx")
if (site_user=="dpmsr"){
Simple_Excel_bg(motifx_all, "MotifX", str_c(dpmsr_set$file$phos, "MotifX_", input$select_data_comp_motif, ".xlsx"))
}
}
return(motifx_all)
}
#--------------------------------------------------------------------------------------------
#--------------------------------------------------------------------------------------------
motifx_calc <- function(s, c, w, FC, ptm_data, parsed_ref, pval_motif, min_seq, pval_filter, fc_filter, comparison){
extractBack_Example <- extractBackground(s, c, w)
# Locate PTMs within full-length proteins and extract neighboring motifs
phindPTMs_Example <- phindPTMs(ptm_data, parsed_ref)
# Reformat foreground sequences for motif-x
foreground_Seqs <- unlist(strsplit(phindPTMs_Example[,"Flank_Seq"], split = "[.]"))
foreground_Seqs_Filtered <- foreground_Seqs[which(lapply(foreground_Seqs, nchar)==15)]
cat(file=stderr(), str_c("Number of foreground sequences for = ", length(foreground_Seqs_Filtered)), "\n")
# Run motif-x using foreground and background sequences from PTMphinder functions above
motifx_data <- try(motifx(foreground_Seqs_Filtered, extractBack_Example, central.res = c, min.seqs = min_seq, pval.cutoff = pval_motif))
if ((!is.null(motifx_data)) & (class(motifx_data) != "try-error")){
motifx_data <- add_column(motifx_data, FC, .before = 1)
motifx_data <- add_column(motifx_data, pval_filter, .before = 1)
motifx_data <- add_column(motifx_data, fc_filter, .before = 1)
motifx_data <- add_column(motifx_data, c, .before = 1)
motifx_data <- add_column(motifx_data, comparison, .before = 1)
names(motifx_data)[1:5] <- c("comparison", "central.res", "foldchange", "pval", "direction")
} else {
motifx_data <- NULL
}
cat(file=stderr(), str_c("Number of motifs for ", c," = ", nrow(motifx_data)), "\n")
if (site_user=="dpmsr"){
Simple_Excel_bg(phindPTMs_Example, "MotifX", str_c(dpmsr_set$file$phos, "MotifX_phindPTM_", comparison, "_", FC, ".xlsx"))
}
return(motifx_data)
}
#--------------------------------------------------------------------------------------------
#--------------------------------------------------------------------------------------------
create_motifx_input <- function(filter_df, parsed_ref, comparison, direction_filter){
#---------Create input file for PTM data ----------------------------------------
MotifPhos <- data.frame(cbind(filter_df$Accession, filter_df$Sequence, filter_df$Modifications))
colnames(MotifPhos) <- c("Accession", "Sequence", "Modifications")
MotifPhos$Accession <- as.character(MotifPhos$Accession)
MotifPhos$Sequence <- as.character(MotifPhos$Sequence)
MotifPhos$Modifications <- as.character(MotifPhos$Modifications)
MotifPhos$Accession <- gsub(";.*", "", MotifPhos$Accession)
MotifPhos <- subset(MotifPhos, Accession != 1000 )
MotifPhos$PhosOnly <- str_extract(MotifPhos$Modifications, "\\dxP.+\\]")
MotifPhos$Total_Sites <- substr(MotifPhos$PhosOnly,0,1)
MotifPhos$PTM_Loc <- str_extract_all(MotifPhos$PhosOnly, "[STY]\\d+")
MotifPhos$PTM_Loc <- gsub("[(]", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub("[)]", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub("[\"]", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub(",", ";", MotifPhos$PTM_Loc)
MotifPhos <- subset(MotifPhos, PTM_Loc != 'character0')
MotifPhos$PTM_Loc <- gsub("c", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub(" ", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Score <- str_extract_all(MotifPhos$PhosOnly, "[(]\\d+\\.*\\d*")
MotifPhos$PTM_Score <- gsub("[(]", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub("[)]", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub("[\"]", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub(",", ";", MotifPhos$PTM_Score)
MotifPhos <- subset(MotifPhos, PTM_Score != 'character0')
MotifPhos$PTM_Score <- gsub("c", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub(" ", "", MotifPhos$PTM_Score)
MotifPhos$Identifier <- str_c("PhosPeptide", seq.int(nrow(MotifPhos)))
df <- data.frame(cbind(MotifPhos$Identifier, MotifPhos$Accession, MotifPhos$Sequence,
MotifPhos$Total_Sites, MotifPhos$PTM_Loc, MotifPhos$PTM_Score))
colnames(df) <- c("Identifier", "Protein_ID", "Peptide_Seq", "Total_Sites", "PTM_Loc", "PTM_Score")
#--------- Subset to insure proteins are in database ----------------------------------------
ptm_data <- df
ptm_data$Protein_ID <- gsub( " .*$", "", ptm_data$Protein_ID)
ptm_data <-subset(ptm_data, Protein_ID %in% parsed_ref$Accession)
if (site_user=="dpmsr"){
cat(file=stderr(), "write ptm_data to excel..." , "\n")
Simple_Excel_bg(ptm_data, "MotifX", str_c(dpmsr_set$file$phos, "MotifX_ptmdata_", comparison, "_", direction_filter, ".xlsx"))
}
return(ptm_data)
}
#--------------------------------------------------------------------------------------------
#--------------------------------------------------------------------------------------------
create_phos_database <- function(session, input, output){
cat(file=stderr(), "Create MotifX sequences start...", "\n")
dpmsr_set$x$motif_set <<- 1
require(stringr)
fasta_path <- parseFilePaths(volumes, input$motif_fasta)
cat(file=stderr(), str_c("fasta_path... ",fasta_path), "\n")
#direct read for legacy dpmsr_set files
#fasta_txt_file <- "/home/dpmsr/shared/mouse.fasta"
fasta_txt_file <- fasta_path$datapath
#raw_fasta <- read.csv2(fasta_txt_file, header=FALSE)
raw_fasta <- data.frame(read_lines(fasta_txt_file) )
raw_fasta <- data.frame(lapply(raw_fasta, function(x) gsub(">sp\\|", ">", x)), stringsAsFactors=F)
if(input$accession_split == "Bar"){
split_char <- "\\|"
}else if(input$accession_split == "Space"){
split_char <- " "
}
# \\| space
colnames(raw_fasta) <- "fasta"
raw_fasta$fasta <- as.character(raw_fasta$fasta)
test_s <- ""
test_a <- ""
find_split <- str_locate(raw_fasta[1,], split_char)
test_a <- c(test_a, substring(raw_fasta[1,], 2, find_split[1]-1))
temp_seq <-""
for (i in 2:nrow(raw_fasta)) {
testa <- substring(raw_fasta[i,],1,1)
if (identical(testa, ">" )) {
find_split <- str_locate(raw_fasta[i,], split_char)
test_a <- c(test_a, substring(raw_fasta[i,], 2, find_split[1]-1) )
test_s <- c(test_s, temp_seq)
temp_seq <- ""
}else{
temp_seq <- str_c(temp_seq, raw_fasta[i,])
}
}
test_s <- c(test_s, temp_seq)
test_a <- as.data.frame(test_a)
test_s <- as.data.frame(test_s)
new_fasta<-(cbind(test_a, test_s))
new_fasta <- as.data.frame(new_fasta[-1,])
colnames(new_fasta) <- c("Accession", "Sequence")
new_fasta$Sequence <- as.character(new_fasta$Sequence)
file_name <- fasta_path$name
file_name <- str_replace(file_name, ".fasta", ".txt")
dpmsr_set$data$phos$background <<- new_fasta
if (site_user=="dpmsr"){
write.csv2(new_fasta, str_c(dpmsr_set$file$phos, file_name), row.names = FALSE)
}
cat(file=stderr(), "Create MotifX sequences end...", "\n")
}
#--------------------------------------------------------------------------------------------
#--------------------------------------------------------------------------------------------
create_phos_database_custom <- function(){
require(stringr)
raw_fasta <- read.csv2("/Users/gregwaitt/Documents/Data/5560_crov2_Sep2020.fasta", header=FALSE)
colnames(raw_fasta) <- "fasta"
raw_fasta$fasta <- as.character(raw_fasta$fasta)
test_s <- ""
test_a <- ""
test_d <- ""
find_split <- str_locate(raw_fasta[1,], " ")
test_a <- c(test_a, substring(raw_fasta[1,], 2, find_split[1]-1))
test_d <- c(test_d, substring(raw_fasta[1,], find_split[1]+1))
temp_seq <-""
for (i in 2:nrow(raw_fasta)) {
testa <- substring(raw_fasta[i,],1,1)
if (identical(testa, ">" )) {
find_split <- str_locate(raw_fasta[i,], " ")
test_a <- c(test_a, substring(raw_fasta[i,], 2, find_split[1]-1) )
test_d <- c(test_d, substring(raw_fasta[i,], find_split[1]+1))
test_s <- c(test_s, temp_seq)
temp_seq <- ""
}else{
temp_seq <- str_c(temp_seq, raw_fasta[i,])
}
}
test_s <- c(test_s, temp_seq)
test_a <- as.data.frame(test_a)
test_d <- as.data.frame(test_d)
test_s <- as.data.frame(test_s)
new_fasta<-(cbind(test_a, test_d, test_s))
new_fasta <- as.data.frame(new_fasta[-1,])
colnames(new_fasta) <- c("Accession", "Description", "Sequence")
new_fasta$Accession <- as.character(new_fasta$Accession)
new_fasta$Description <- as.character(new_fasta$Description)
new_fasta$Sequence <- as.character(new_fasta$Sequence)
if (site_user=="dpmsr"){
Simple_Excel_bg(new_fasta, "MotifX", "5560_crov2_Sep2020.xlsx")
}
}
#--------------------------------------------------------------------------------------------
#--------------------------------------------------------------------------------------------
#--------------------------------------------------------------------------------------------
testonly <- function(){
parsed_ref <- parsed_refx
s <- sx
w <- wx
pval_motif <- pval_motifx
data_in <- data_inx
parsed_ref <- dpmsr_set$data$phos$background
names(parsed_ref) <- c("V1", "V2")
s <- list(parsed_ref$Sequence)
s <- unlist(s)
s <- unlist(parsed_ref[,2])
extractBack_Example <- extractBackground(s, "S", 15)
filter_df <- subset(data_in, data_in$Stats == "Up" )
FC <- "Up"
ptm_data <- create_motifx_input(filter_df, parsed_ref)
motifx_S <- motifx_calc(s, "S", w, "Up", ptm_data, parsed_ref, pval_motif, input$pvalue_cutoff, input$foldchange_cutoff, input$select_data_comp_motif)
test_parsed_ref <- read.table("Mmusculus_110419.txt", header=FALSE, row.names=NULL, sep="\t")
test_s <- unlist(test_parsed_ref[,2])
extractBack_Example <- extractBackground(test_s, "S", 15)
parsed_ref <- dpmsr_set$data$phos$background
names(parsed_ref) <- c("V1", "V2")
parsed_ref <- rbind(c("Accession", "Sequence"), parsed_ref)
s <- unlist(parsed_ref[,2])
extractBack_Example <- extractBackground(s, "S", 15)
s<-parsed_ref$Sequence
}
#--------------------------------------------------------------------------------------------
create_padded_seq <- function(){
filter_df <- dpmsr_set$data$final$sltmm
parsed_ref <- dpmsr_set$data$phos$background
#---------Create input file for PTM data ----------------------------------------
MotifPhos <- data.frame(cbind(filter_df$Accession, filter_df$Sequence, filter_df$Modifications))
colnames(MotifPhos) <- c("Accession", "Sequence", "Modifications")
MotifPhos$Accession <- as.character(MotifPhos$Accession)
MotifPhos$Sequence <- as.character(MotifPhos$Sequence)
MotifPhos$Modifications <- as.character(MotifPhos$Modifications)
MotifPhos$Accession <- gsub(";.*", "", MotifPhos$Accession)
MotifPhos <- subset(MotifPhos, Accession != 1000 )
MotifPhos$PhosOnly <- str_extract(MotifPhos$Modifications, "\\dxP.+\\]")
MotifPhos$Total_Sites <- substr(MotifPhos$PhosOnly,0,1)
MotifPhos$PTM_Loc <- str_extract_all(MotifPhos$PhosOnly, "[STY]\\d+")
MotifPhos$PTM_Loc <- gsub("[(]", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub("[)]", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub("[\"]", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub(",", ";", MotifPhos$PTM_Loc)
MotifPhos <- subset(MotifPhos, PTM_Loc != 'character0')
MotifPhos$PTM_Loc <- gsub("c", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Loc <- gsub(" ", "", MotifPhos$PTM_Loc)
MotifPhos$PTM_Score <- str_extract_all(MotifPhos$PhosOnly, "[(]\\d+\\.*\\d*")
MotifPhos$PTM_Score <- gsub("[(]", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub("[)]", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub("[\"]", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub(",", ";", MotifPhos$PTM_Score)
MotifPhos <- subset(MotifPhos, PTM_Score != 'character0')
MotifPhos$PTM_Score <- gsub("c", "", MotifPhos$PTM_Score)
MotifPhos$PTM_Score <- gsub(" ", "", MotifPhos$PTM_Score)
MotifPhos$Identifier <- str_c("PhosPeptide", seq.int(nrow(MotifPhos)))
df <- data.frame(cbind(MotifPhos$Identifier, MotifPhos$Accession, MotifPhos$Sequence,
MotifPhos$Total_Sites, MotifPhos$PTM_Loc, MotifPhos$PTM_Score))
colnames(df) <- c("Identifier", "Protein_ID", "Peptide_Seq", "Total_Sites", "PTM_Loc", "PTM_Score")
#--------- Subset to insure proteins are in database ----------------------------------------
ptm_data <- df
ptm_data$Protein_ID <- gsub( " .*$", "", ptm_data$Protein_ID)
ptm_data <-subset(ptm_data, Protein_ID %in% parsed_ref$Accession)
if (site_user=="dpmsr"){
cat(file=stderr(), "write ptm_data to excel..." , "\n")
Simple_Excel_bg(ptm_data, "MotifX", str_c(dpmsr_set$file$phos, "Padded_Seq.xlsx"))
}
phindPTMs_Example <- phindPTMs(ptm_data, parsed_ref)
df_PTMs <- data.frame(phindPTMs_Example)
ptm_data$Prot_Loc <- df_PTMs$Prot_Loc
ptm_data$Flank_Seq <- df_PTMs$Flank_Seq
ptm_data$Ambiguity <- df_PTMs$Ambiguity
ptm_data$Prot_Seq <- df_PTMs$Prot_Seq
if (site_user=="dpmsr"){
Simple_Excel_bg(ptm_data, "MotifX", str_c(dpmsr_set$file$phos, "Padded_Seq.xlsx"))
}
return(ptm_data)
}