R/Rcolombos.R
In onertipaday/Rcolombos: Interface to Colombos Compendia using the Exposed REST API
#' This method mimics the quick_search functionality of Colombos.
#' It takes a string containg the nickname for the selected organism and a vector of string
#' representing the genes of interest for the specified organism and returns a list containing
#' the locustags (gene_names), contrasts and M-values for the current selection.
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param genes A vector of strings representing the genes of interest.
#' @param geneNames boolean if == FALSE (default) returns the locustag otherwise the gene_name for the selected genes.
#'
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
#' @examples
#' \dontrun{
#' library("Rcolombos")
#' my_module <- quick_search(organism="ecoli",
#' genes=c("b0400","b2805","b0567"),
#' geneNames=FALSE)
#' heatmap(as.matrix(my_module), col=terrain.colors(15))
#' }
#'
quick_search <- function(organism="ecoli", genes, geneNames=FALSE){
if(is.null(genes)) stop("Insert a character vector with the genes to be imputed.") else {}
r <- GET("http://rest.colombos.fmach.it/", path = paste("quick_search",organism, paste(genes, collapse=","), sep="/"))
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(tmp$data$Mvalues),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
#' This method mimics the advanced_search functionality of Colombos.
#' It takes a series of parameters, representing the different settings available on Colombos advanced search
#' and returns a list containing the locustags (gene_names), contrasts and M-values for the current selection.
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param g_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param c_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param by A string eithes genes, contrasts, both allowing the selection by genes entities, contrast entities or both.
#' @param g_search_type A string either genes, go or annotation.
#' @param ann_type A string containing the selected gene_annotation_type: use \code{\link{listEntities}} to display the available entities.
#' @param c_search_type A string either contrast_names. experiment, go, condition use \code{\link{listOrganisms}} to display
#' the available organisms.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
#' @examples
#' \dontrun{
#' library("Rcolombos")
#'
#' # modules by gene entities
#' g.gn <- advanced_search(organism="bsubt",
#' g_ids=c("cgeB","yfnG"),
#' by="genes", g_search_type="genes")
#' g.go <- advanced_search(organism="bsubt",
#' g_ids="response to antibiotic, transcription",
#' by="genes", g_search_type="go")
#' g.anno <- advanced_search(organism="bsubt",
#' g_ids="biotin-carboxyl carrier protein assembly",
#' by="genes", g_search_type="annotation", ann_type="Pathway")
#'
#' # modules by contrast entities
#' c.cn <- advanced_search(organism="bsubt",
#' c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2"),
#' by="contrasts", c_search_type="contrast_names")
#' c.go <- advanced_search(organism="bsubt",
#' c_ids="response to antibiotic, transcription",
#' by="contrasts", c_search_type="go")
#' c.exp <- advanced_search(organism="bsubt",
#' c_ids="GSE22296", by="contrasts", c_search_type="experiment")
#' c.cond <- advanced_search(organism="bsubt",
#' c_ids=c("DAPTOMYCIN","H2O2","HPUra","IPTG","MMC","MNCL2","MOENOMYCIN","RAMOPLANIN"),
#' by="contrasts", c_search_type="condition")
#'
#' # modules by both gene and contrast entities
#' b.go.cn <- advanced_search(organism="bsubt",
#' g_ids="response to antibiotic, transcription", geneNames=F,
#' c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2"),
#' g_search_type="go", c_search_type="contrast_names", by="both")
#' b.gn.ge <- advanced_search(organism="bsubt", g_ids=c("BSU00020","BSU00100"),
#' geneNames=F, c_ids="GSE22296", g_search_type="genes",
#' c_search_type="experiment", by="both")
#' b.go.ge <- advanced_search(organism="bsubt", g_ids="response to antibiotic, transcription",
#' geneNames=F, c_ids="GSE22296", g_search_type="go",
#' c_search_type="experiment", by="both")
#' b.gn.cn <- advanced_search(organism="bsubt",
#' g_ids=c("dnaA","dnaN","yaaA","recF","yaaB","gyrB"), geneNames=FALSE,
#' c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2",
#' "GSM27219.ch2-vs-GSM27219.ch1","GSM27278.ch2-vs-GSM27278.ch1",
#' "GSM27279.ch1-vs-GSM27279.ch2"),
#' g_search_type="genes", c_search_type="contrast_names", by="both")
#' heatmap(as.matrix(b.gn.cn), col=terrain.colors(15))
#' }
#'
advanced_search <- function(organism=NULL, g_ids=NULL, geneNames=FALSE, c_ids, by="genes", g_search_type, ann_type, c_search_type){
if(is.null(organism)) stop("Insert a character vector corresponding to the nickname of the selected organism.") else {}
if(by=="genes") out <- advanced_search_by_genes(organism, g_ids, geneNames, g_search_type, ann_type)
else if(by=="contrasts") out <- advanced_search_by_contrasts(organism, c_ids, geneNames, c_search_type)
else if(by=="both") out <- advanced_search_by_both(organism, g_ids, geneNames, c_ids, g_search_type, ann_type, c_search_type)
else stop("Wrong by: it should be either genes, contrasts or both!")
}
#' Accessory function allowing the advanced_search by gene_ids, go, annotation
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param ids A vector of strings representing gene_id, go terms or annotation entities according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param g_search_type A string either genes, go or annotation.
#' @param ann_type A string containing the selected gene_annotation_type: use \code{\link{listEntities}} to display the available entities.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
advanced_search_by_genes <- function(organism="bsubt", ids=NULL, geneNames=FALSE, g_search_type="genes", ann_type){
if(is.null(ids)) stop("Insert the ids for the specific search_type.") else {}
if(g_search_type=="genes"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_genes", organism, "genes", paste(ids, collapse=","), sep="/")
}
else if(g_search_type=="go"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_genes", organism, "go", gsub(" ","%20", ids), sep="/")
}
else if(g_search_type=="annotation"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_genes", organism, "annotation", gsub(" ","%20", ann_type),
gsub(" ","%20", ids), sep="/")
} else {
stop("Wrong search_type: it should be either genes, go or annotation!")
}
r <- GET(url_string)
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(tmp$data$Mvalues),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
#' Accessory function allowing the advanced_search by contrast_ids, go, experiment, condition
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param c_search_type A string either contrast_names. experiment, go, condition.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
advanced_search_by_contrasts <- function(organism=NULL, ids=NULL, geneNames=FALSE, c_search_type=NULL){
if(is.null(ids)) stop("Insert the ids for the specific search_type.") else {}
if(c_search_type=="contrast_names"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "contrast_names", paste(ids, collapse=","), sep="/")
}
else if(c_search_type=="experiment"){
# url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "experiment", paste(gsub(" ","%20", ids), collapse=","), sep="/")
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "experiment", gsub(" ","%20", ids), sep="/")
}
else if(c_search_type=="go"){
# url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "go", paste(gsub(" ","%20", ids), collapse=","), sep="/")
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "go", gsub(" ","%20", ids), sep="/")
}
else if(c_search_type=="condition"){
# url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "condition", paste(gsub(" ","%20", ids), collapse=","), sep="/")
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "condition", paste(ids, collapse=","), sep="/")
} else {
stop("Wrong search_type: it should be either contrast_names, experiment, go or condition!")
}
r <- GET(url_string)
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(sapply(tmp$data$Mvalues, as.character)),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
#' Accessory function allowing the advanced_search by both g_ids and c_ids
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param g_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param c_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param g_search_type A string either genes, go or annotation.
#' @param ann_type A string containing the selected gene_annotation_type: use \code{\link{listEntities}} to display the available entities.
#' @param c_search_type A string either contrast_names. experiment, go, condition.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
advanced_search_by_both <- function(organism, g_ids, geneNames, c_ids, g_search_type, ann_type, c_search_type){
if(is.null(g_ids)) stop("Insert a character vector with the g_ids to be imputed.") else {}
if(is.null(c_ids)) stop("Insert a character vector with the c_ids to be imputed.") else {}
base_url <- "http://rest.colombos.fmach.it/advanced_search_by_both"
if(g_search_type=="genes"){
g_string <- paste(base_url, organism, "genes", paste(g_ids, collapse=","), sep="/")
}
else if(g_search_type=="go"){
g_string <- paste(base_url, organism, "go", gsub(" ","%20", g_ids), sep="/")
}
else if(g_search_type=="annotation"){
g_string <- paste(base_url, organism, "annotation", gsub(" ","%20", ann_type),
gsub(" ","%20", g_ids), sep="/")
} else {
stop("Wrong search_type: it should be either genes, go or annotation!")
}
#
if(c_search_type=="contrast_names"){
url_string <- paste(g_string, "contrast_names", paste(c_ids, collapse=","), sep="/")
}
else if(c_search_type=="experiment"){
# url_string <- paste(g_string, "experiment", paste(gsub(" ","%20", c_ids), collapse=","), sep="/")
url_string <- paste(g_string, "experiment", gsub(" ","%20", c_ids), sep="/")
}
else if(c_search_type=="go"){
# url_string <- paste(g_string, "go", paste(gsub(" ","%20", c_ids), collapse=","), sep="/")
url_string <- paste(g_string, "go", gsub(" ","%20", c_ids), sep="/")
}
else if(c_search_type=="condition"){
# url_string <- paste(g_string, "condition", paste(gsub(" ","%20", c_ids), collapse=","), sep="/")
url_string <- paste(g_string, "condition", paste(c_ids, collapse=","), sep="/")
} else {
stop("Wrong search_type: it should be either contrast_names, experiment, go or condition!")
}
r <- GET(url_string)
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(sapply(tmp$data$Mvalues, as.character)),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
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#' This method mimics the quick_search functionality of Colombos.
#' It takes a string containg the nickname for the selected organism and a vector of string
#' representing the genes of interest for the specified organism and returns a list containing
#' the locustags (gene_names), contrasts and M-values for the current selection.
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param genes A vector of strings representing the genes of interest.
#' @param geneNames boolean if == FALSE (default) returns the locustag otherwise the gene_name for the selected genes.
#'
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
#' @examples
#' \dontrun{
#' library("Rcolombos")
#' my_module <- quick_search(organism="ecoli",
#' genes=c("b0400","b2805","b0567"),
#' geneNames=FALSE)
#' heatmap(as.matrix(my_module), col=terrain.colors(15))
#' }
#'
quick_search <- function(organism="ecoli", genes, geneNames=FALSE){
if(is.null(genes)) stop("Insert a character vector with the genes to be imputed.") else {}
r <- GET("http://rest.colombos.fmach.it/", path = paste("quick_search",organism, paste(genes, collapse=","), sep="/"))
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(tmp$data$Mvalues),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
#' This method mimics the advanced_search functionality of Colombos.
#' It takes a series of parameters, representing the different settings available on Colombos advanced search
#' and returns a list containing the locustags (gene_names), contrasts and M-values for the current selection.
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param g_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param c_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param by A string eithes genes, contrasts, both allowing the selection by genes entities, contrast entities or both.
#' @param g_search_type A string either genes, go or annotation.
#' @param ann_type A string containing the selected gene_annotation_type: use \code{\link{listEntities}} to display the available entities.
#' @param c_search_type A string either contrast_names. experiment, go, condition use \code{\link{listOrganisms}} to display
#' the available organisms.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
#' @examples
#' \dontrun{
#' library("Rcolombos")
#'
#' # modules by gene entities
#' g.gn <- advanced_search(organism="bsubt",
#' g_ids=c("cgeB","yfnG"),
#' by="genes", g_search_type="genes")
#' g.go <- advanced_search(organism="bsubt",
#' g_ids="response to antibiotic, transcription",
#' by="genes", g_search_type="go")
#' g.anno <- advanced_search(organism="bsubt",
#' g_ids="biotin-carboxyl carrier protein assembly",
#' by="genes", g_search_type="annotation", ann_type="Pathway")
#'
#' # modules by contrast entities
#' c.cn <- advanced_search(organism="bsubt",
#' c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2"),
#' by="contrasts", c_search_type="contrast_names")
#' c.go <- advanced_search(organism="bsubt",
#' c_ids="response to antibiotic, transcription",
#' by="contrasts", c_search_type="go")
#' c.exp <- advanced_search(organism="bsubt",
#' c_ids="GSE22296", by="contrasts", c_search_type="experiment")
#' c.cond <- advanced_search(organism="bsubt",
#' c_ids=c("DAPTOMYCIN","H2O2","HPUra","IPTG","MMC","MNCL2","MOENOMYCIN","RAMOPLANIN"),
#' by="contrasts", c_search_type="condition")
#'
#' # modules by both gene and contrast entities
#' b.go.cn <- advanced_search(organism="bsubt",
#' g_ids="response to antibiotic, transcription", geneNames=F,
#' c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2"),
#' g_search_type="go", c_search_type="contrast_names", by="both")
#' b.gn.ge <- advanced_search(organism="bsubt", g_ids=c("BSU00020","BSU00100"),
#' geneNames=F, c_ids="GSE22296", g_search_type="genes",
#' c_search_type="experiment", by="both")
#' b.go.ge <- advanced_search(organism="bsubt", g_ids="response to antibiotic, transcription",
#' geneNames=F, c_ids="GSE22296", g_search_type="go",
#' c_search_type="experiment", by="both")
#' b.gn.cn <- advanced_search(organism="bsubt",
#' g_ids=c("dnaA","dnaN","yaaA","recF","yaaB","gyrB"), geneNames=FALSE,
#' c_ids=c("GSM27217.ch2-vs-GSM27217.ch1","GSM27218.ch1-vs-GSM27218.ch2",
#' "GSM27219.ch2-vs-GSM27219.ch1","GSM27278.ch2-vs-GSM27278.ch1",
#' "GSM27279.ch1-vs-GSM27279.ch2"),
#' g_search_type="genes", c_search_type="contrast_names", by="both")
#' heatmap(as.matrix(b.gn.cn), col=terrain.colors(15))
#' }
#'
advanced_search <- function(organism=NULL, g_ids=NULL, geneNames=FALSE, c_ids, by="genes", g_search_type, ann_type, c_search_type){
if(is.null(organism)) stop("Insert a character vector corresponding to the nickname of the selected organism.") else {}
if(by=="genes") out <- advanced_search_by_genes(organism, g_ids, geneNames, g_search_type, ann_type)
else if(by=="contrasts") out <- advanced_search_by_contrasts(organism, c_ids, geneNames, c_search_type)
else if(by=="both") out <- advanced_search_by_both(organism, g_ids, geneNames, c_ids, g_search_type, ann_type, c_search_type)
else stop("Wrong by: it should be either genes, contrasts or both!")
}
#' Accessory function allowing the advanced_search by gene_ids, go, annotation
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param ids A vector of strings representing gene_id, go terms or annotation entities according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param g_search_type A string either genes, go or annotation.
#' @param ann_type A string containing the selected gene_annotation_type: use \code{\link{listEntities}} to display the available entities.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
advanced_search_by_genes <- function(organism="bsubt", ids=NULL, geneNames=FALSE, g_search_type="genes", ann_type){
if(is.null(ids)) stop("Insert the ids for the specific search_type.") else {}
if(g_search_type=="genes"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_genes", organism, "genes", paste(ids, collapse=","), sep="/")
}
else if(g_search_type=="go"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_genes", organism, "go", gsub(" ","%20", ids), sep="/")
}
else if(g_search_type=="annotation"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_genes", organism, "annotation", gsub(" ","%20", ann_type),
gsub(" ","%20", ids), sep="/")
} else {
stop("Wrong search_type: it should be either genes, go or annotation!")
}
r <- GET(url_string)
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(tmp$data$Mvalues),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
#' Accessory function allowing the advanced_search by contrast_ids, go, experiment, condition
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param c_search_type A string either contrast_names. experiment, go, condition.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
advanced_search_by_contrasts <- function(organism=NULL, ids=NULL, geneNames=FALSE, c_search_type=NULL){
if(is.null(ids)) stop("Insert the ids for the specific search_type.") else {}
if(c_search_type=="contrast_names"){
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "contrast_names", paste(ids, collapse=","), sep="/")
}
else if(c_search_type=="experiment"){
# url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "experiment", paste(gsub(" ","%20", ids), collapse=","), sep="/")
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "experiment", gsub(" ","%20", ids), sep="/")
}
else if(c_search_type=="go"){
# url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "go", paste(gsub(" ","%20", ids), collapse=","), sep="/")
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "go", gsub(" ","%20", ids), sep="/")
}
else if(c_search_type=="condition"){
# url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "condition", paste(gsub(" ","%20", ids), collapse=","), sep="/")
url_string <- paste("http://rest.colombos.fmach.it/advanced_search_by_contrast", organism, "condition", paste(ids, collapse=","), sep="/")
} else {
stop("Wrong search_type: it should be either contrast_names, experiment, go or condition!")
}
r <- GET(url_string)
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(sapply(tmp$data$Mvalues, as.character)),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
#' Accessory function allowing the advanced_search by both g_ids and c_ids
#'
#' @param organism A character containing the organism id: use \code{\link{listOrganisms}} to display
#' the available organisms.
#' @param g_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param geneNames boolean if == FALSE (default) return the locustag otherwise the gene_name for the selected genes.
#' @param c_ids A vector of strings representing contrast_id, go terms, experiment id or condition id according the search type.
#' @param g_search_type A string either genes, go or annotation.
#' @param ann_type A string containing the selected gene_annotation_type: use \code{\link{listEntities}} to display the available entities.
#' @param c_search_type A string either contrast_names. experiment, go, condition.
#'
#' @return A data.frame containing locustag (gene_names),
#' contrasts and M-values for the current organism and genes.
#'
#' @references http://colombos.net
#'
#' @export
#'
advanced_search_by_both <- function(organism, g_ids, geneNames, c_ids, g_search_type, ann_type, c_search_type){
if(is.null(g_ids)) stop("Insert a character vector with the g_ids to be imputed.") else {}
if(is.null(c_ids)) stop("Insert a character vector with the c_ids to be imputed.") else {}
base_url <- "http://rest.colombos.fmach.it/advanced_search_by_both"
if(g_search_type=="genes"){
g_string <- paste(base_url, organism, "genes", paste(g_ids, collapse=","), sep="/")
}
else if(g_search_type=="go"){
g_string <- paste(base_url, organism, "go", gsub(" ","%20", g_ids), sep="/")
}
else if(g_search_type=="annotation"){
g_string <- paste(base_url, organism, "annotation", gsub(" ","%20", ann_type),
gsub(" ","%20", g_ids), sep="/")
} else {
stop("Wrong search_type: it should be either genes, go or annotation!")
}
#
if(c_search_type=="contrast_names"){
url_string <- paste(g_string, "contrast_names", paste(c_ids, collapse=","), sep="/")
}
else if(c_search_type=="experiment"){
# url_string <- paste(g_string, "experiment", paste(gsub(" ","%20", c_ids), collapse=","), sep="/")
url_string <- paste(g_string, "experiment", gsub(" ","%20", c_ids), sep="/")
}
else if(c_search_type=="go"){
# url_string <- paste(g_string, "go", paste(gsub(" ","%20", c_ids), collapse=","), sep="/")
url_string <- paste(g_string, "go", gsub(" ","%20", c_ids), sep="/")
}
else if(c_search_type=="condition"){
# url_string <- paste(g_string, "condition", paste(gsub(" ","%20", c_ids), collapse=","), sep="/")
url_string <- paste(g_string, "condition", paste(c_ids, collapse=","), sep="/")
} else {
stop("Wrong search_type: it should be either contrast_names, experiment, go or condition!")
}
r <- GET(url_string)
if (r$status_code != 200) {
stop_for_status(r)
} else {
tmp <- content(r)
response = suppressWarnings( data.frame(matrix(as.numeric(sapply(tmp$data$Mvalues, as.character)),
nrow=length(tmp$data$geneLocustags), ncol=length(tmp$data$contrasts), byrow=T)) )
colnames(response) <- tmp$data$contrasts; rownames(response) <- tmp$data$geneLocustags
if (geneNames) rownames(response) <- tmp$data$geneNames
return(response)
}
}
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