R/transition for cellDesigner.R
In SysBioChalmers/FALCONET: FAst visuaLisation of COmputational NETworks
Defines functions
produceInputForCellDesigner
DefineProtein
DeProteinConnect
DefineAllMet
getOtherProduct
getOtherReactant
getReactionMain
getGeneAnnotation
getProAnnotation
getAnnotation
getPosition
getNewSize
Documented in
DefineAllMet
DefineProtein
DeProteinConnect
getAnnotation
getGeneAnnotation
getNewSize
getOtherProduct
getOtherReactant
getPosition
getProAnnotation
getReactionMain
produceInputForCellDesigner
#-----------------------------------------------------------------------
#prepare the component for the cellDesigner
#------------------------------------------------------------------------
#' Define the size of graph
#'
#'
#' @param x a value determining the length of graph
#' @param y a value determining the height of graph
#'
#' @return
#' @export txt a part of SBML file
#'
#' @examples
getNewSize <- function(x=600,y=400){
txt <- vector()
txt[1] <- "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
txt[2] <- "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">"
txt[3] <- "<model metaid=\"Acetate_space_utilization\" id=\"Acetate_space_utilization\">"
txt[4] <- "<notes>"
txt[5] <- "<html xmlns=\"http://www.w3.org/1999/xhtml\">"
txt[6] <- "<head>"
txt[7] <- "<title/>"
txt[8] <- "</head>"
txt[9] <- "<body>The prokaryotic utilization of acetate and its interconversion to acetyl-CoA. Acetate and acetyl-CoA can function as a carbon source for energy production. Website=www.biocyc.org/Ecoli/Pathways/free text=Voet and Voet (textbook) Biochemistry"
txt[10] <- "</body>"
txt[11] <- "</html>"
txt[12] <- "</notes>"
txt[13] <- "<annotation>"
txt[14] <- "<celldesigner:extension>"
txt[15] <- "<celldesigner:modelVersion>4.0</celldesigner:modelVersion>"
txt[16] <- paste("<celldesigner:modelDisplay sizeX=\"",x,"\" sizeY=\"",y,"\"/>",sep="")
txt[17] <- "<celldesigner:listOfCompartmentAliases/>"
txt[18] <- "<celldesigner:listOfComplexSpeciesAliases/>"
txt[19] <- "<celldesigner:listOfSpeciesAliases>"
return(txt)
}
#' Define position information for each metabolite
#'
#'
#' @param id01 id of a component
#' @param species01 species id of a component
#' @param x01 x coordinate of a component
#' @param y01 y coordinate of a component
#'
#' @return
#' @export txt a part of SBML file with coordinate of the component in a map
#'
#' @examples
getPosition <- function(id01,species01,x01,y01){
txt <- vector()
txt[1] <- paste("<celldesigner:speciesAlias id=\"",id01,"\" species=\"",species01,"\">", sep = "")
txt[2] <- "<celldesigner:activity>inactive</celldesigner:activity>"
txt[3] <- paste("<celldesigner:bounds x=\"",x01,"\" y=\"",y01,"\" w=\"70.0\" h=\"25.0\"/>", sep = "")
txt[4] <- "<celldesigner:font size=\"12\"/>"
txt[5] <- "<celldesigner:view state=\"usual\"/>"
txt[6] <- "<celldesigner:usualView>"
txt[7] <- "<celldesigner:innerPosition x=\"0.0\" y=\"0.0\"/>"
txt[8] <- "<celldesigner:boxSize width=\"70.0\" height=\"25.0\"/>"
txt[9] <- "<celldesigner:singleLine width=\"1.0\"/>"
txt[10] <- "<celldesigner:paint color=\"ffccff66\" scheme=\"Color\"/>"
txt[11] <- "</celldesigner:usualView>"
txt[12] <- "<celldesigner:briefView>"
txt[13] <- "<celldesigner:innerPosition x=\"0.0\" y=\"0.0\"/>"
txt[14] <- "<celldesigner:boxSize width=\"80.0\" height=\"60.0\"/>"
txt[15] <- "<celldesigner:singleLine width=\"0.0\"/>"
txt[16] <- "<celldesigner:paint color=\"3fff0000\" scheme=\"Color\"/>"
txt[17] <- "</celldesigner:briefView>"
txt[18] <- "<celldesigner:info state=\"empty\" angle=\"-1.5707963267948966\"/>"
txt[19] <- "</celldesigner:speciesAlias>"
return(txt)
}
#' Define annotation information for each metabolite
#'
#'
#' @param species01 species id of a component
#' @param name01 name of a component
#'
#' @return
#' @export txt a part of SBML file with name of the component in a map
#'
#' @examples
getAnnotation <- function(species01,name01){
##class_type: SIMPLE_MOLECULE,PROTEIN, GENE
txt <- vector()
txt[1] <- paste("<species metaid=\"",species01,"\" id=\"",species01,"\" name=\"",name01,"\" compartment=\"default\" initialAmount=\"0\">",sep = "")
txt[2] <- "<annotation>"
txt[3] <- "<celldesigner:extension>"
txt[4] <- "<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>"
txt[5] <- "<celldesigner:speciesIdentity>"
txt[6] <- "<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>"
txt[7] <- paste("<celldesigner:name>",name01,"</celldesigner:name>", sep = "")
txt[8] <- "</celldesigner:speciesIdentity>"
txt[9] <- "</celldesigner:extension>"
txt[10] <- "</annotation>"
txt[11] <- "</species>"
return(txt)
}
#' Define annotation information for each protein
#'
#'
#' @param species01 species id of protein
#' @param name01 name of a component
#' @param proteinID01 ID of the protein as the component
#'
#' @return
#' @export txt a part of SBML file with protein annotation for the related component
#'
#' @examples
getProAnnotation <- function(species01,name01, proteinID01){
##class_type: SIMPLE_MOLECULE,PROTEIN, GENE
txt <- vector()
txt[1] <- paste("<species metaid=\"",species01,"\" id=\"",species01,"\" name=\"",name01,"\" compartment=\"default\" initialAmount=\"0\">", sep="")
txt[2] <- "<annotation>"
txt[3] <- "<celldesigner:extension>"
txt[4] <- "<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>"
txt[5] <- "<celldesigner:speciesIdentity>"
txt[6] <- "<celldesigner:class>PROTEIN</celldesigner:class>"
txt[7] <- paste("<celldesigner:proteinReference>",proteinID01,"</celldesigner:proteinReference>", sep="")
txt[8] <- "</celldesigner:speciesIdentity>"
txt[9] <- "</celldesigner:extension>"
txt[10] <- "</annotation>"
txt[11] <- "</species>"
return(txt)
}
#' Define annotation information for each gene
#'
#'
#' @param species01 specie id of gene
#' @param name01 name of a component
#' @param geneID01 ID of the gene as the component
#'
#' @return
#' @export txt a part of SBML file with gene annotation for the related component
#'
#' @examples
getGeneAnnotation <- function(species01,name01, geneID01){
txt <- vector()
txt[1] <- paste("<species metaid=\"",species01,"\" id=\"",species01,"\" name=\"",name01,"\" compartment=\"default\" initialAmount=\"0\">", sep = "")
txt[2] <- "<annotation>"
txt[3] <- "<celldesigner:extension>"
txt[4] <- "<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>"
txt[5] <- "<celldesigner:speciesIdentity>"
txt[6] <- "<celldesigner:class>GENE</celldesigner:class>"
txt[7] <- paste("<celldesigner:geneReference>",geneID01,"</celldesigner:geneReference>", sep="")
txt[8] <- "</celldesigner:speciesIdentity>"
txt[9] <- "</celldesigner:extension>"
txt[10] <- "</annotation>"
txt[11] <- "</species>"
return(txt)
}
#-----------------------------------------------------------------------
#prepare the rxn connection for the cellDesigner
#------------------------------------------------------------------------
#' The output of the followed function could be replaced of R1
#' This function is used to define the base reactant and production information for each reaction
#'
#' @param rxnID
#' @param BR_specie specie id for the base reactant
#' @param BR_id id for the base reactant
#' @param BP_specie specie id for the base product
#' @param BP_id id for the base product
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
getReactionMain <- function(rxnID, BR_specie, BR_id, BP_specie, BP_id ){
txt0 <- vector()
txt0[1] <- paste("<reaction metaid=\"", rxnID, "\" id=\"", rxnID, "\" reversible=\"false\">", sep = "")
txt0[2] <- "<annotation>"
txt0[3] <- "<celldesigner:extension>"
txt0[4] <- "<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>"
txt0[5] <- "<celldesigner:baseReactants>"
txt0[6] <- paste("<celldesigner:baseReactant species=\"", BR_specie, "\" alias=\"", BR_id, "\">", sep = "")
#txt0[7] <- "<celldesigner:linkAnchor position=\"E\"/>" ##define how the metabolite is connected??
txt0[7] <- "</celldesigner:baseReactant>"
txt0[8] <- "</celldesigner:baseReactants>"
txt0[9] <- "<celldesigner:baseProducts>"
txt0[10] <- paste("<celldesigner:baseProduct species=\"",BP_specie, "\" alias=\"", BP_id, "\">", sep = "")
#txt0[11] <- "<celldesigner:linkAnchor position=\"W\"/>" ##define how the metabolite is connected??
txt0[11] <- "</celldesigner:baseProduct>"
txt0[12] <- "</celldesigner:baseProducts>"
txt0[13] <- "<celldesigner:listOfReactantLinks>"
return(txt0)
}
#' The output of the followed function could be replaced of R2
#' The function is used to define the other reactant (except the base reactant) in a reaction
#'
#' @param R_specie specie id for the reactant
#' @param R_id id for the reactant
#'
#' @return
#' @export
#'
#' @examples
getOtherReactant <- function(R_specie, R_id ){
txt0 <- vector()
txt0[1] <- paste("<celldesigner:reactantLink reactant=\"",R_specie,"\" alias=\"",R_id,"\" targetLineIndex=\"-1,0\">", sep="")
#txt0[2] <- "<celldesigner:linkAnchor position=\"E\"/>" ##define how the metabolite is connected??
txt0[2] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[3] <- "<celldesigner:listOfLineDirection>"
txt0[4] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[5] <- "</celldesigner:listOfLineDirection>"
txt0[6] <- "</celldesigner:connectScheme>"
txt0[7] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\" type=\"Straight\"/>"
txt0[8] <- "</celldesigner:reactantLink>"
return(txt0)
}
#' The function is used to define the other product (except the base product) in a reaction
#'
#' @param P_specie specie id for the product
#' @param P_id id for the product
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
getOtherProduct <- function(P_specie, P_id ){
txt0 <- vector()
txt0[1] <- paste("<celldesigner:productLink product=\"",P_specie,"\" alias=\"",P_id,"\" targetLineIndex=\"-1,1\">",sep="")
#txt0[2] <- "<celldesigner:linkAnchor position=\"W\"/>" ##define how the metabolite is connected??
txt0[2] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[3] <- "<celldesigner:listOfLineDirection>"
txt0[4] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[5] <- "</celldesigner:listOfLineDirection>"
txt0[6] <- "</celldesigner:connectScheme>"
txt0[7] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\" type=\"Straight\"/>"
txt0[8] <- "</celldesigner:productLink>"
return(txt0)
}
#' The function is used to define the met in SBML file
#'
#' @param specie specie id for the metabolite
#' @param id id for the metabolite
#' @param Metaid meta id for the metabolite
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
DefineAllMet <- function(specie, id, Metaid){
txt0 <- vector()
txt0[1] <- paste("<speciesReference metaid=\"",Metaid,"\" species=\"",specie,"\">", sep="")
txt0[2] <- "<annotation>"
txt0[3] <- "<celldesigner:extension>"
txt0[4] <- paste("<celldesigner:alias>",id,"</celldesigner:alias>", sep="")
txt0[5] <- "</celldesigner:extension>"
txt0[6] <- "</annotation>"
txt0[7] <- "</speciesReference>"
return(txt0)
}
#' The function is used to define the connection of general gene id and protein id with each reaction
#'
#' @param p_specie specie id for the protein
#' @param p_id id for the protein
#' @param g_specie specie id for the gene
#' @param g_id id for the gene
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
DeProteinConnect <- function(p_specie, p_id, g_specie, g_id){
txt0 <- vector()
txt0[1] <- "</celldesigner:listOfProductLinks>"
txt0[2] <- "<celldesigner:connectScheme connectPolicy=\"direct\" rectangleIndex=\"0\">"
txt0[3] <- "<celldesigner:listOfLineDirection>"
txt0[4] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[5] <- "</celldesigner:listOfLineDirection>"
txt0[6] <- "</celldesigner:connectScheme>"
txt0[7] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\"/>"
txt0[8] <- "<celldesigner:listOfModification>"
txt0[9] <- paste("<celldesigner:modification type=\"CATALYSIS\" modifiers=\"",p_specie,"\" aliases=\"",p_id,"\" targetLineIndex=\"-1,4\">", sep = "")
txt0[10] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[11] <- "<celldesigner:listOfLineDirection>"
txt0[12] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[13] <- "</celldesigner:listOfLineDirection>"
txt0[14] <- "</celldesigner:connectScheme>"
txt0[15] <- paste("<celldesigner:linkTarget species=\"",p_specie,"\" alias=\"",p_id,"\">", sep = "")
#txt0[16] <- "<celldesigner:linkAnchor position=\"S\"/>" ##define how the metabolite is connected??
txt0[16] <- "</celldesigner:linkTarget>"
txt0[17] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\"/>"
txt0[18] <- "</celldesigner:modification>"
txt0[19] <- paste("<celldesigner:modification type=\"CATALYSIS\" modifiers=\"",g_specie,"\" aliases=\"",g_id,"\" targetLineIndex=\"-1,5\">", sep = "")
txt0[20] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[21] <- "<celldesigner:listOfLineDirection>"
txt0[22] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[23] <- "</celldesigner:listOfLineDirection>"
txt0[24] <- "</celldesigner:connectScheme>"
txt0[25] <- paste("<celldesigner:linkTarget species=\"",g_specie,"\" alias=\"",g_id,"\">", sep = "")
#txt0[27] <- "<celldesigner:linkAnchor position=\"S\"/>" ##define how the metabolite is connected??
txt0[26] <- "</celldesigner:linkTarget>"
txt0[27] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\"/>"
txt0[28] <- "</celldesigner:modification>"
txt0[29] <- "</celldesigner:listOfModification>"
txt0[30] <- "</celldesigner:extension>"
txt0[31] <- "</annotation>"
txt0[32] <- "<listOfReactants>"
return(txt0)
}
#' The function is used to define the general ID information of gene and protein in SMBL file
#'
#' @param p_specie specie id for protein
#' @param p_id id for protein
#' @param p_metaid meta id for protein
#' @param g_specie specia id for gene
#' @param g_id id for gene
#' @param g_metaid meta id for gene
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
DefineProtein <- function(p_specie, p_id, p_metaid, g_specie, g_id, g_metaid){
txt0 <- vector()
txt0[1] <- "</listOfProducts>"
txt0[2] <- "<listOfModifiers>"
txt0[3] <- paste("<modifierSpeciesReference metaid=\"",p_metaid,"\" species=\"",p_specie,"\">", sep = "")
txt0[4] <- "<annotation>"
txt0[5] <- "<celldesigner:extension>"
txt0[6] <- paste("<celldesigner:alias>",p_id,"</celldesigner:alias>", sep = "")
txt0[7] <- "</celldesigner:extension>"
txt0[8] <- "</annotation>"
txt0[9] <- "</modifierSpeciesReference>"
txt0[10] <- paste("<modifierSpeciesReference metaid=\"",g_metaid,"\" species=\"",g_specie,"\">", sep = "")
txt0[11] <- "<annotation>"
txt0[12] <- "<celldesigner:extension>"
txt0[13] <- paste("<celldesigner:alias>",g_id,"</celldesigner:alias>", sep = "")
txt0[14] <- "</celldesigner:extension>"
txt0[15] <- "</annotation>"
txt0[16] <- "</modifierSpeciesReference>"
txt0[17] <- "</listOfModifiers>"
txt0[18] <- "</reaction>"
return(txt0)
}
#' Define the reaction metaid, baseReactant and baseProduct in cellDesigner
#'
#' @param rxn0 a dataframe contains the rxn annotation
#' @param rxn_p a dataframe contains the general id information of gene and protein for each reaction
#' @param R30 the template file of cellDesigner file
#' @param R70 the template file of cellDesigner file
#'
#' @return
#' @export txt6_new a part of SMBL file contains eaction metaid, baseReactant and baseProduct in cellDesigner
#'
#' @examples
getRxnInformation <- function (rxn0, rxn_p, R30=R3,R70=R7){ #input a datafram contains the detailed reaction information
#
#test
#rxn0 = rxn_annotation[[1]]
#rxn_p = gpr[[1]]
#rxn0$note[3]
rxnID <- rxn0$rxnID[1]
BR_specie <- rxn0$specie[ which(rxn0$type=="reactant" & rxn0$note=="base")]
BR_id <- rxn0$id[ which(rxn0$type=="reactant" & rxn0$note=="base")]
BP_specie <- rxn0$specie[ which(rxn0$type=="product" & rxn0$note=="base")]
BP_id <- rxn0$id[ which(rxn0$type=="product" & rxn0$note=="base")]
txt6_R1 <- getReactionMain(rxnID,BR_specie,BR_id,BP_specie,BP_id)
#define other repeated Reactants in cellDesigner
if(length(which(rxn0$type=="reactant" & rxn0$note != "base"))){
otherReactantID <- which(rxn0$type=="reactant" & rxn0$note != "base") ##should be careful about this result
txt6_R2 <- vector()
R_specie <- rxn0$specie[otherReactantID]
R_id <- rxn0$id[otherReactantID]
txt6_R2 <- vector()
for (i in seq(length((otherReactantID)))){
txt6_R2 <- c(txt6_R2,getOtherReactant(R_specie[i], R_id[i]))
}
} else{
txt6_R2 <- NULL
}
txt6_R3 <- R30
#define other repeated Products in cellDesigner
if(length(which(rxn0$type=="product" & rxn0$note != "base"))){
otherProductID <- which(rxn0$type=="product" & rxn0$note != "base")
txt6_R4 <- vector()
P_specie <- rxn0$specie[otherProductID]
P_id <- rxn0$id[otherProductID]
txt6_R4 <- vector()
for (i in seq(length(otherProductID))){
txt6_R4 <- c(txt6_R4,getOtherProduct(P_specie[i], P_id[i]))
}
} else{
txt6_R4 <- NULL
}
txt6_R5 <- DeProteinConnect(rxn_p$protein_specie,rxn_p$protein_id, rxn_p$gene_specie,rxn_p$gene_id)
#define all reactants information
if(length(which(rxn0$type=="reactant"))){
reactantID <- which(rxn0$type=="reactant")
specie_r <- rxn0$specie[reactantID]
id_r <- rxn0$id[reactantID]
MetaID_r <- rxn0$MetaID[reactantID]
txt6_R6 <- vector()
for (i in seq(length(reactantID))){
txt6_R6 <- c(txt6_R6,DefineAllMet(specie_r[i], id_r[i], MetaID_r[i]))
}
} else{
txt6_R6 <- ""
}
txt6_R7 <-R70
#define all products information
if(length(which(rxn0$type=="product"))){
productID <- which(rxn0$type=="product")
specie_p <- rxn0$specie[productID]
id_p <- rxn0$id[productID]
MetaID_p <- rxn0$MetaID[productID]
txt6_R8 <- vector()
for (i in seq(length(productID))){
txt6_R8 <- c(txt6_R8,DefineAllMet(specie_p[i], id_p[i], MetaID_p[i]))
}
} else{
txt6_R8 <- ""
}
txt6_R9 <- DefineProtein(rxn_p$protein_specie,rxn_p$protein_id, rxn_p$MetaID_p, rxn_p$gene_specie,rxn_p$gene_id, rxn_p$MetaID_g)
txt6_new <- c(txt6_R1,txt6_R2,txt6_R3,txt6_R4,txt6_R5,txt6_R6,txt6_R7,txt6_R8,txt6_R9)
return(txt6_new)
}
#' The function is used to produce the cell designer file
#'
#' @param met_annotation_inf a dataframe contains the met annotation of the chose reaction
#' @param gpr_inf a dataframe contains the GPR information of the chose reaction
#' @param rxn_core_carbon_inf a dataframe contains the detailed rxn annotation
#' @param x_size a number define the width of graph
#' @param y_size a number define the height of graph
#'
#' @return
#' @export txt_new a SBML file
#'
#' @examples
produceInputForCellDesigner <- function(met_annotation_inf,
gpr_inf,
rxn_core_carbon_inf,
x_size=2500,
y_size=3600) {
# this script is used to input the coordinate of metaoblite, protein and gene into celldesigner
# Input the comon template
txt1 <- readLines(file("data/template1")) # model information and size
txt3 <- readLines(file("data/template3")) # other information of model besides metabolits and reactions
txt5 <- readLines(file("data/template5")) # sign of xml format
txt7 <- readLines(file("data/template7")) # end sign of xml format
txt1 <- getNewSize(x = 2500, y = 3600)
txt2 <- vector()
txt3 <- vector()
txt4 <- vector()
#--------------------------------------
# txt2
#--------------------------------------
id <- met_annotation_inf$id
species <- met_annotation_inf$species
name <- met_annotation_inf$name
x <- as.character(met_annotation_inf$x)
y <- as.character(met_annotation_inf$y)
for (i in seq(length(id))) {
txt2 <- c(getPosition(id01 = id[i], species01 = species[i], x01 = x[i], y01 = y[i]), txt2)
}
#--------------------------------------
# txt3
#--------------------------------------
## add protein define
## add gene define
## input protein and gene information
protein0 <- filter(met_annotation_inf, type == "PROTEIN")
protein0$type <- "GENERIC"
# protein0$protein_id <- paste("pr",1:length(protein0$metID), sep="")
protein0$protein_id <- str_replace_all(protein0$rxnID, "r_", "pr")
gene0 <- filter(met_annotation_inf, type == "GENE")
# gene0$gene_id <- paste("gn",1:length(gene0$metID), sep="")
gene0$gene_id <- str_replace_all(gene0$rxnID, "r_", "gn")
getProteinGene <- function(id, type, name) {
txt0 <- vector()
if (type == "GENERIC") {
txt0[1] <- paste("<celldesigner:protein id=\"", id, "\" name=\"", name, "\" type=\"GENERIC\"/>", sep = "")
}
if (type == "GENE") {
txt0[1] <- paste("<celldesigner:gene id=\"", id, "\" name=\"", name, "\" type=\"GENE\"/>", sep = "")
}
return(txt0)
}
txt3_1 <- readLines(file("data/txt3_1.xml"))
# txt3_2 protein module
protein_id <- protein0$protein_id
type_p <- protein0$type
name_p <- protein0$name
txt3_2 <- vector()
for (i in seq(length(protein_id))) {
txt3_2 <- c(txt3_2, getProteinGene(id = protein_id[i], type = type_p[i], name = name_p[i]))
}
txt3_3 <- readLines(file("data/txt3_3.xml"))
# txt3_4 gene module
gene_id <- gene0$gene_id
type_g <- gene0$type
name_g <- gene0$name
txt3_4 <- vector()
for (i in seq(length(gene_id))) {
txt3_4 <- c(txt3_4, getProteinGene(id = gene_id[i], type = type_g[i], name = name_g[i]))
}
txt3_5 <- readLines(file("data/txt3_5.xml"))
txt30 <- c(txt3_1, txt3_2, txt3_3, txt3_4, txt3_5)
#--------------------------------------------------------------------------
## txt4: give the annotation for each unique metabolite
#--------------------------------------------------------------------------
# txt4_1 metabolite module
met_without_protein0 <- filter(met_annotation_inf, type == "SIMPLE_MOLECULE")
species_unique <- unique(met_without_protein0$species)
name_unique <- unique(met_without_protein0$name)
txt4_1 <- vector()
for (i in seq(length(species_unique))) {
txt4_1 <- c(txt4_1, getAnnotation(species01 = species_unique[i], name01 = name_unique[i]))
}
# txt4_2 protein module
protein_specie <- protein0$species
protein_id <- protein0$protein_id
type_p <- protein0$type
name_p <- protein0$name
txt4_2 <- vector()
for (i in seq(length(protein_id))) {
txt4_2 <- c(txt4_2, getProAnnotation(species01 = protein_specie[i], name01 = name_p[i], proteinID01 = protein_id[i]))
}
# txt4_3 gene module
gene_id <- gene0$gene_id
gene_specie <- gene0$species
type_g <- gene0$type
name_g <- gene0$name
txt4_3 <- vector()
for (i in seq(length(gene_id))) {
txt4_3 <- c(txt4_3, getGeneAnnotation(species01 = gene_specie[i], name01 = name_g[i], geneID01 = gene_id[i]))
}
txt4 <- c(txt4_1, txt4_2, txt4_3)
# merge the above file
txt_final0 <- c(txt1, txt2, txt30, txt4, txt5, txt7)
#----------------------------------------------------------
# txt6 Input the connection of metabolite into celldesigner
#---------------------------------------------------------
# input the common template
R3 <- readLines(file("data/txt6_repeated_part3")) # connect two parts
R5 <- readLines(file("data/txt6_repeated_part5.xml")) # mainly define connectScheme____version2
R7 <- readLines(file("data/txt6_repeated_part7")) # connect two parts
rxn <- rxn_core_carbon_inf
rxn_p0 <- gpr_inf
## change reaction into list format
## data process before using function
rxnID <- unique(rxn$rxnID)
rxn_annotation <- list()
rxn_id <- list()
for (i in 1:length(rxnID)) {
rxn_id[[i]] <- which(rxn$rxnID %in% rxnID[i] == TRUE)
rxn_annotation[[i]] <- rxn[rxn_id[[i]], ]
}
gpr0 <- list()
for (i in 1:length(rxn_p0$rxnID)) {
gpr0[[i]] <- rxn_p0[i, ]
}
## using the main function
txt6_new <- vector()
for (j in 1:length(rxnID)) {
txt6_new <- c(txt6_new, getRxnInformation(rxn_annotation[[j]], rxn_p = gpr0[[j]], R30=R3,R70=R7))
}
txt_new <- c(txt1, txt2, txt30, txt4, txt5, txt6_new, txt7) # connect each template
# save the file
# only with component coordinate
writeLines(txt_final0, file("result/model_add_metabolite_protein.xml")) # save
# adding the component connection
writeLines(txt_new, file("result/model_with_protein-add rxn connection.xml")) # save
}
SysBioChalmers/FALCONET documentation built on Dec. 5, 2020, 11:35 a.m.
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Defines functions produceInputForCellDesigner DefineProtein DeProteinConnect DefineAllMet getOtherProduct getOtherReactant getReactionMain getGeneAnnotation getProAnnotation getAnnotation getPosition getNewSize
Documented in DefineAllMet DefineProtein DeProteinConnect getAnnotation getGeneAnnotation getNewSize getOtherProduct getOtherReactant getPosition getProAnnotation getReactionMain produceInputForCellDesigner
#-----------------------------------------------------------------------
#prepare the component for the cellDesigner
#------------------------------------------------------------------------
#' Define the size of graph
#'
#'
#' @param x a value determining the length of graph
#' @param y a value determining the height of graph
#'
#' @return
#' @export txt a part of SBML file
#'
#' @examples
getNewSize <- function(x=600,y=400){
txt <- vector()
txt[1] <- "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
txt[2] <- "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">"
txt[3] <- "<model metaid=\"Acetate_space_utilization\" id=\"Acetate_space_utilization\">"
txt[4] <- "<notes>"
txt[5] <- "<html xmlns=\"http://www.w3.org/1999/xhtml\">"
txt[6] <- "<head>"
txt[7] <- "<title/>"
txt[8] <- "</head>"
txt[9] <- "<body>The prokaryotic utilization of acetate and its interconversion to acetyl-CoA. Acetate and acetyl-CoA can function as a carbon source for energy production. Website=www.biocyc.org/Ecoli/Pathways/free text=Voet and Voet (textbook) Biochemistry"
txt[10] <- "</body>"
txt[11] <- "</html>"
txt[12] <- "</notes>"
txt[13] <- "<annotation>"
txt[14] <- "<celldesigner:extension>"
txt[15] <- "<celldesigner:modelVersion>4.0</celldesigner:modelVersion>"
txt[16] <- paste("<celldesigner:modelDisplay sizeX=\"",x,"\" sizeY=\"",y,"\"/>",sep="")
txt[17] <- "<celldesigner:listOfCompartmentAliases/>"
txt[18] <- "<celldesigner:listOfComplexSpeciesAliases/>"
txt[19] <- "<celldesigner:listOfSpeciesAliases>"
return(txt)
}
#' Define position information for each metabolite
#'
#'
#' @param id01 id of a component
#' @param species01 species id of a component
#' @param x01 x coordinate of a component
#' @param y01 y coordinate of a component
#'
#' @return
#' @export txt a part of SBML file with coordinate of the component in a map
#'
#' @examples
getPosition <- function(id01,species01,x01,y01){
txt <- vector()
txt[1] <- paste("<celldesigner:speciesAlias id=\"",id01,"\" species=\"",species01,"\">", sep = "")
txt[2] <- "<celldesigner:activity>inactive</celldesigner:activity>"
txt[3] <- paste("<celldesigner:bounds x=\"",x01,"\" y=\"",y01,"\" w=\"70.0\" h=\"25.0\"/>", sep = "")
txt[4] <- "<celldesigner:font size=\"12\"/>"
txt[5] <- "<celldesigner:view state=\"usual\"/>"
txt[6] <- "<celldesigner:usualView>"
txt[7] <- "<celldesigner:innerPosition x=\"0.0\" y=\"0.0\"/>"
txt[8] <- "<celldesigner:boxSize width=\"70.0\" height=\"25.0\"/>"
txt[9] <- "<celldesigner:singleLine width=\"1.0\"/>"
txt[10] <- "<celldesigner:paint color=\"ffccff66\" scheme=\"Color\"/>"
txt[11] <- "</celldesigner:usualView>"
txt[12] <- "<celldesigner:briefView>"
txt[13] <- "<celldesigner:innerPosition x=\"0.0\" y=\"0.0\"/>"
txt[14] <- "<celldesigner:boxSize width=\"80.0\" height=\"60.0\"/>"
txt[15] <- "<celldesigner:singleLine width=\"0.0\"/>"
txt[16] <- "<celldesigner:paint color=\"3fff0000\" scheme=\"Color\"/>"
txt[17] <- "</celldesigner:briefView>"
txt[18] <- "<celldesigner:info state=\"empty\" angle=\"-1.5707963267948966\"/>"
txt[19] <- "</celldesigner:speciesAlias>"
return(txt)
}
#' Define annotation information for each metabolite
#'
#'
#' @param species01 species id of a component
#' @param name01 name of a component
#'
#' @return
#' @export txt a part of SBML file with name of the component in a map
#'
#' @examples
getAnnotation <- function(species01,name01){
##class_type: SIMPLE_MOLECULE,PROTEIN, GENE
txt <- vector()
txt[1] <- paste("<species metaid=\"",species01,"\" id=\"",species01,"\" name=\"",name01,"\" compartment=\"default\" initialAmount=\"0\">",sep = "")
txt[2] <- "<annotation>"
txt[3] <- "<celldesigner:extension>"
txt[4] <- "<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>"
txt[5] <- "<celldesigner:speciesIdentity>"
txt[6] <- "<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>"
txt[7] <- paste("<celldesigner:name>",name01,"</celldesigner:name>", sep = "")
txt[8] <- "</celldesigner:speciesIdentity>"
txt[9] <- "</celldesigner:extension>"
txt[10] <- "</annotation>"
txt[11] <- "</species>"
return(txt)
}
#' Define annotation information for each protein
#'
#'
#' @param species01 species id of protein
#' @param name01 name of a component
#' @param proteinID01 ID of the protein as the component
#'
#' @return
#' @export txt a part of SBML file with protein annotation for the related component
#'
#' @examples
getProAnnotation <- function(species01,name01, proteinID01){
##class_type: SIMPLE_MOLECULE,PROTEIN, GENE
txt <- vector()
txt[1] <- paste("<species metaid=\"",species01,"\" id=\"",species01,"\" name=\"",name01,"\" compartment=\"default\" initialAmount=\"0\">", sep="")
txt[2] <- "<annotation>"
txt[3] <- "<celldesigner:extension>"
txt[4] <- "<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>"
txt[5] <- "<celldesigner:speciesIdentity>"
txt[6] <- "<celldesigner:class>PROTEIN</celldesigner:class>"
txt[7] <- paste("<celldesigner:proteinReference>",proteinID01,"</celldesigner:proteinReference>", sep="")
txt[8] <- "</celldesigner:speciesIdentity>"
txt[9] <- "</celldesigner:extension>"
txt[10] <- "</annotation>"
txt[11] <- "</species>"
return(txt)
}
#' Define annotation information for each gene
#'
#'
#' @param species01 specie id of gene
#' @param name01 name of a component
#' @param geneID01 ID of the gene as the component
#'
#' @return
#' @export txt a part of SBML file with gene annotation for the related component
#'
#' @examples
getGeneAnnotation <- function(species01,name01, geneID01){
txt <- vector()
txt[1] <- paste("<species metaid=\"",species01,"\" id=\"",species01,"\" name=\"",name01,"\" compartment=\"default\" initialAmount=\"0\">", sep = "")
txt[2] <- "<annotation>"
txt[3] <- "<celldesigner:extension>"
txt[4] <- "<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>"
txt[5] <- "<celldesigner:speciesIdentity>"
txt[6] <- "<celldesigner:class>GENE</celldesigner:class>"
txt[7] <- paste("<celldesigner:geneReference>",geneID01,"</celldesigner:geneReference>", sep="")
txt[8] <- "</celldesigner:speciesIdentity>"
txt[9] <- "</celldesigner:extension>"
txt[10] <- "</annotation>"
txt[11] <- "</species>"
return(txt)
}
#-----------------------------------------------------------------------
#prepare the rxn connection for the cellDesigner
#------------------------------------------------------------------------
#' The output of the followed function could be replaced of R1
#' This function is used to define the base reactant and production information for each reaction
#'
#' @param rxnID
#' @param BR_specie specie id for the base reactant
#' @param BR_id id for the base reactant
#' @param BP_specie specie id for the base product
#' @param BP_id id for the base product
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
getReactionMain <- function(rxnID, BR_specie, BR_id, BP_specie, BP_id ){
txt0 <- vector()
txt0[1] <- paste("<reaction metaid=\"", rxnID, "\" id=\"", rxnID, "\" reversible=\"false\">", sep = "")
txt0[2] <- "<annotation>"
txt0[3] <- "<celldesigner:extension>"
txt0[4] <- "<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>"
txt0[5] <- "<celldesigner:baseReactants>"
txt0[6] <- paste("<celldesigner:baseReactant species=\"", BR_specie, "\" alias=\"", BR_id, "\">", sep = "")
#txt0[7] <- "<celldesigner:linkAnchor position=\"E\"/>" ##define how the metabolite is connected??
txt0[7] <- "</celldesigner:baseReactant>"
txt0[8] <- "</celldesigner:baseReactants>"
txt0[9] <- "<celldesigner:baseProducts>"
txt0[10] <- paste("<celldesigner:baseProduct species=\"",BP_specie, "\" alias=\"", BP_id, "\">", sep = "")
#txt0[11] <- "<celldesigner:linkAnchor position=\"W\"/>" ##define how the metabolite is connected??
txt0[11] <- "</celldesigner:baseProduct>"
txt0[12] <- "</celldesigner:baseProducts>"
txt0[13] <- "<celldesigner:listOfReactantLinks>"
return(txt0)
}
#' The output of the followed function could be replaced of R2
#' The function is used to define the other reactant (except the base reactant) in a reaction
#'
#' @param R_specie specie id for the reactant
#' @param R_id id for the reactant
#'
#' @return
#' @export
#'
#' @examples
getOtherReactant <- function(R_specie, R_id ){
txt0 <- vector()
txt0[1] <- paste("<celldesigner:reactantLink reactant=\"",R_specie,"\" alias=\"",R_id,"\" targetLineIndex=\"-1,0\">", sep="")
#txt0[2] <- "<celldesigner:linkAnchor position=\"E\"/>" ##define how the metabolite is connected??
txt0[2] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[3] <- "<celldesigner:listOfLineDirection>"
txt0[4] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[5] <- "</celldesigner:listOfLineDirection>"
txt0[6] <- "</celldesigner:connectScheme>"
txt0[7] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\" type=\"Straight\"/>"
txt0[8] <- "</celldesigner:reactantLink>"
return(txt0)
}
#' The function is used to define the other product (except the base product) in a reaction
#'
#' @param P_specie specie id for the product
#' @param P_id id for the product
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
getOtherProduct <- function(P_specie, P_id ){
txt0 <- vector()
txt0[1] <- paste("<celldesigner:productLink product=\"",P_specie,"\" alias=\"",P_id,"\" targetLineIndex=\"-1,1\">",sep="")
#txt0[2] <- "<celldesigner:linkAnchor position=\"W\"/>" ##define how the metabolite is connected??
txt0[2] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[3] <- "<celldesigner:listOfLineDirection>"
txt0[4] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[5] <- "</celldesigner:listOfLineDirection>"
txt0[6] <- "</celldesigner:connectScheme>"
txt0[7] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\" type=\"Straight\"/>"
txt0[8] <- "</celldesigner:productLink>"
return(txt0)
}
#' The function is used to define the met in SBML file
#'
#' @param specie specie id for the metabolite
#' @param id id for the metabolite
#' @param Metaid meta id for the metabolite
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
DefineAllMet <- function(specie, id, Metaid){
txt0 <- vector()
txt0[1] <- paste("<speciesReference metaid=\"",Metaid,"\" species=\"",specie,"\">", sep="")
txt0[2] <- "<annotation>"
txt0[3] <- "<celldesigner:extension>"
txt0[4] <- paste("<celldesigner:alias>",id,"</celldesigner:alias>", sep="")
txt0[5] <- "</celldesigner:extension>"
txt0[6] <- "</annotation>"
txt0[7] <- "</speciesReference>"
return(txt0)
}
#' The function is used to define the connection of general gene id and protein id with each reaction
#'
#' @param p_specie specie id for the protein
#' @param p_id id for the protein
#' @param g_specie specie id for the gene
#' @param g_id id for the gene
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
DeProteinConnect <- function(p_specie, p_id, g_specie, g_id){
txt0 <- vector()
txt0[1] <- "</celldesigner:listOfProductLinks>"
txt0[2] <- "<celldesigner:connectScheme connectPolicy=\"direct\" rectangleIndex=\"0\">"
txt0[3] <- "<celldesigner:listOfLineDirection>"
txt0[4] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[5] <- "</celldesigner:listOfLineDirection>"
txt0[6] <- "</celldesigner:connectScheme>"
txt0[7] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\"/>"
txt0[8] <- "<celldesigner:listOfModification>"
txt0[9] <- paste("<celldesigner:modification type=\"CATALYSIS\" modifiers=\"",p_specie,"\" aliases=\"",p_id,"\" targetLineIndex=\"-1,4\">", sep = "")
txt0[10] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[11] <- "<celldesigner:listOfLineDirection>"
txt0[12] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[13] <- "</celldesigner:listOfLineDirection>"
txt0[14] <- "</celldesigner:connectScheme>"
txt0[15] <- paste("<celldesigner:linkTarget species=\"",p_specie,"\" alias=\"",p_id,"\">", sep = "")
#txt0[16] <- "<celldesigner:linkAnchor position=\"S\"/>" ##define how the metabolite is connected??
txt0[16] <- "</celldesigner:linkTarget>"
txt0[17] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\"/>"
txt0[18] <- "</celldesigner:modification>"
txt0[19] <- paste("<celldesigner:modification type=\"CATALYSIS\" modifiers=\"",g_specie,"\" aliases=\"",g_id,"\" targetLineIndex=\"-1,5\">", sep = "")
txt0[20] <- "<celldesigner:connectScheme connectPolicy=\"direct\">"
txt0[21] <- "<celldesigner:listOfLineDirection>"
txt0[22] <- "<celldesigner:lineDirection index=\"0\" value=\"unknown\"/>"
txt0[23] <- "</celldesigner:listOfLineDirection>"
txt0[24] <- "</celldesigner:connectScheme>"
txt0[25] <- paste("<celldesigner:linkTarget species=\"",g_specie,"\" alias=\"",g_id,"\">", sep = "")
#txt0[27] <- "<celldesigner:linkAnchor position=\"S\"/>" ##define how the metabolite is connected??
txt0[26] <- "</celldesigner:linkTarget>"
txt0[27] <- "<celldesigner:line width=\"1.0\" color=\"ff000000\"/>"
txt0[28] <- "</celldesigner:modification>"
txt0[29] <- "</celldesigner:listOfModification>"
txt0[30] <- "</celldesigner:extension>"
txt0[31] <- "</annotation>"
txt0[32] <- "<listOfReactants>"
return(txt0)
}
#' The function is used to define the general ID information of gene and protein in SMBL file
#'
#' @param p_specie specie id for protein
#' @param p_id id for protein
#' @param p_metaid meta id for protein
#' @param g_specie specia id for gene
#' @param g_id id for gene
#' @param g_metaid meta id for gene
#'
#' @return
#' @export txt0 a part of SBML file
#'
#' @examples
DefineProtein <- function(p_specie, p_id, p_metaid, g_specie, g_id, g_metaid){
txt0 <- vector()
txt0[1] <- "</listOfProducts>"
txt0[2] <- "<listOfModifiers>"
txt0[3] <- paste("<modifierSpeciesReference metaid=\"",p_metaid,"\" species=\"",p_specie,"\">", sep = "")
txt0[4] <- "<annotation>"
txt0[5] <- "<celldesigner:extension>"
txt0[6] <- paste("<celldesigner:alias>",p_id,"</celldesigner:alias>", sep = "")
txt0[7] <- "</celldesigner:extension>"
txt0[8] <- "</annotation>"
txt0[9] <- "</modifierSpeciesReference>"
txt0[10] <- paste("<modifierSpeciesReference metaid=\"",g_metaid,"\" species=\"",g_specie,"\">", sep = "")
txt0[11] <- "<annotation>"
txt0[12] <- "<celldesigner:extension>"
txt0[13] <- paste("<celldesigner:alias>",g_id,"</celldesigner:alias>", sep = "")
txt0[14] <- "</celldesigner:extension>"
txt0[15] <- "</annotation>"
txt0[16] <- "</modifierSpeciesReference>"
txt0[17] <- "</listOfModifiers>"
txt0[18] <- "</reaction>"
return(txt0)
}
#' Define the reaction metaid, baseReactant and baseProduct in cellDesigner
#'
#' @param rxn0 a dataframe contains the rxn annotation
#' @param rxn_p a dataframe contains the general id information of gene and protein for each reaction
#' @param R30 the template file of cellDesigner file
#' @param R70 the template file of cellDesigner file
#'
#' @return
#' @export txt6_new a part of SMBL file contains eaction metaid, baseReactant and baseProduct in cellDesigner
#'
#' @examples
getRxnInformation <- function (rxn0, rxn_p, R30=R3,R70=R7){ #input a datafram contains the detailed reaction information
#
#test
#rxn0 = rxn_annotation[[1]]
#rxn_p = gpr[[1]]
#rxn0$note[3]
rxnID <- rxn0$rxnID[1]
BR_specie <- rxn0$specie[ which(rxn0$type=="reactant" & rxn0$note=="base")]
BR_id <- rxn0$id[ which(rxn0$type=="reactant" & rxn0$note=="base")]
BP_specie <- rxn0$specie[ which(rxn0$type=="product" & rxn0$note=="base")]
BP_id <- rxn0$id[ which(rxn0$type=="product" & rxn0$note=="base")]
txt6_R1 <- getReactionMain(rxnID,BR_specie,BR_id,BP_specie,BP_id)
#define other repeated Reactants in cellDesigner
if(length(which(rxn0$type=="reactant" & rxn0$note != "base"))){
otherReactantID <- which(rxn0$type=="reactant" & rxn0$note != "base") ##should be careful about this result
txt6_R2 <- vector()
R_specie <- rxn0$specie[otherReactantID]
R_id <- rxn0$id[otherReactantID]
txt6_R2 <- vector()
for (i in seq(length((otherReactantID)))){
txt6_R2 <- c(txt6_R2,getOtherReactant(R_specie[i], R_id[i]))
}
} else{
txt6_R2 <- NULL
}
txt6_R3 <- R30
#define other repeated Products in cellDesigner
if(length(which(rxn0$type=="product" & rxn0$note != "base"))){
otherProductID <- which(rxn0$type=="product" & rxn0$note != "base")
txt6_R4 <- vector()
P_specie <- rxn0$specie[otherProductID]
P_id <- rxn0$id[otherProductID]
txt6_R4 <- vector()
for (i in seq(length(otherProductID))){
txt6_R4 <- c(txt6_R4,getOtherProduct(P_specie[i], P_id[i]))
}
} else{
txt6_R4 <- NULL
}
txt6_R5 <- DeProteinConnect(rxn_p$protein_specie,rxn_p$protein_id, rxn_p$gene_specie,rxn_p$gene_id)
#define all reactants information
if(length(which(rxn0$type=="reactant"))){
reactantID <- which(rxn0$type=="reactant")
specie_r <- rxn0$specie[reactantID]
id_r <- rxn0$id[reactantID]
MetaID_r <- rxn0$MetaID[reactantID]
txt6_R6 <- vector()
for (i in seq(length(reactantID))){
txt6_R6 <- c(txt6_R6,DefineAllMet(specie_r[i], id_r[i], MetaID_r[i]))
}
} else{
txt6_R6 <- ""
}
txt6_R7 <-R70
#define all products information
if(length(which(rxn0$type=="product"))){
productID <- which(rxn0$type=="product")
specie_p <- rxn0$specie[productID]
id_p <- rxn0$id[productID]
MetaID_p <- rxn0$MetaID[productID]
txt6_R8 <- vector()
for (i in seq(length(productID))){
txt6_R8 <- c(txt6_R8,DefineAllMet(specie_p[i], id_p[i], MetaID_p[i]))
}
} else{
txt6_R8 <- ""
}
txt6_R9 <- DefineProtein(rxn_p$protein_specie,rxn_p$protein_id, rxn_p$MetaID_p, rxn_p$gene_specie,rxn_p$gene_id, rxn_p$MetaID_g)
txt6_new <- c(txt6_R1,txt6_R2,txt6_R3,txt6_R4,txt6_R5,txt6_R6,txt6_R7,txt6_R8,txt6_R9)
return(txt6_new)
}
#' The function is used to produce the cell designer file
#'
#' @param met_annotation_inf a dataframe contains the met annotation of the chose reaction
#' @param gpr_inf a dataframe contains the GPR information of the chose reaction
#' @param rxn_core_carbon_inf a dataframe contains the detailed rxn annotation
#' @param x_size a number define the width of graph
#' @param y_size a number define the height of graph
#'
#' @return
#' @export txt_new a SBML file
#'
#' @examples
produceInputForCellDesigner <- function(met_annotation_inf,
gpr_inf,
rxn_core_carbon_inf,
x_size=2500,
y_size=3600) {
# this script is used to input the coordinate of metaoblite, protein and gene into celldesigner
# Input the comon template
txt1 <- readLines(file("data/template1")) # model information and size
txt3 <- readLines(file("data/template3")) # other information of model besides metabolits and reactions
txt5 <- readLines(file("data/template5")) # sign of xml format
txt7 <- readLines(file("data/template7")) # end sign of xml format
txt1 <- getNewSize(x = 2500, y = 3600)
txt2 <- vector()
txt3 <- vector()
txt4 <- vector()
#--------------------------------------
# txt2
#--------------------------------------
id <- met_annotation_inf$id
species <- met_annotation_inf$species
name <- met_annotation_inf$name
x <- as.character(met_annotation_inf$x)
y <- as.character(met_annotation_inf$y)
for (i in seq(length(id))) {
txt2 <- c(getPosition(id01 = id[i], species01 = species[i], x01 = x[i], y01 = y[i]), txt2)
}
#--------------------------------------
# txt3
#--------------------------------------
## add protein define
## add gene define
## input protein and gene information
protein0 <- filter(met_annotation_inf, type == "PROTEIN")
protein0$type <- "GENERIC"
# protein0$protein_id <- paste("pr",1:length(protein0$metID), sep="")
protein0$protein_id <- str_replace_all(protein0$rxnID, "r_", "pr")
gene0 <- filter(met_annotation_inf, type == "GENE")
# gene0$gene_id <- paste("gn",1:length(gene0$metID), sep="")
gene0$gene_id <- str_replace_all(gene0$rxnID, "r_", "gn")
getProteinGene <- function(id, type, name) {
txt0 <- vector()
if (type == "GENERIC") {
txt0[1] <- paste("<celldesigner:protein id=\"", id, "\" name=\"", name, "\" type=\"GENERIC\"/>", sep = "")
}
if (type == "GENE") {
txt0[1] <- paste("<celldesigner:gene id=\"", id, "\" name=\"", name, "\" type=\"GENE\"/>", sep = "")
}
return(txt0)
}
txt3_1 <- readLines(file("data/txt3_1.xml"))
# txt3_2 protein module
protein_id <- protein0$protein_id
type_p <- protein0$type
name_p <- protein0$name
txt3_2 <- vector()
for (i in seq(length(protein_id))) {
txt3_2 <- c(txt3_2, getProteinGene(id = protein_id[i], type = type_p[i], name = name_p[i]))
}
txt3_3 <- readLines(file("data/txt3_3.xml"))
# txt3_4 gene module
gene_id <- gene0$gene_id
type_g <- gene0$type
name_g <- gene0$name
txt3_4 <- vector()
for (i in seq(length(gene_id))) {
txt3_4 <- c(txt3_4, getProteinGene(id = gene_id[i], type = type_g[i], name = name_g[i]))
}
txt3_5 <- readLines(file("data/txt3_5.xml"))
txt30 <- c(txt3_1, txt3_2, txt3_3, txt3_4, txt3_5)
#--------------------------------------------------------------------------
## txt4: give the annotation for each unique metabolite
#--------------------------------------------------------------------------
# txt4_1 metabolite module
met_without_protein0 <- filter(met_annotation_inf, type == "SIMPLE_MOLECULE")
species_unique <- unique(met_without_protein0$species)
name_unique <- unique(met_without_protein0$name)
txt4_1 <- vector()
for (i in seq(length(species_unique))) {
txt4_1 <- c(txt4_1, getAnnotation(species01 = species_unique[i], name01 = name_unique[i]))
}
# txt4_2 protein module
protein_specie <- protein0$species
protein_id <- protein0$protein_id
type_p <- protein0$type
name_p <- protein0$name
txt4_2 <- vector()
for (i in seq(length(protein_id))) {
txt4_2 <- c(txt4_2, getProAnnotation(species01 = protein_specie[i], name01 = name_p[i], proteinID01 = protein_id[i]))
}
# txt4_3 gene module
gene_id <- gene0$gene_id
gene_specie <- gene0$species
type_g <- gene0$type
name_g <- gene0$name
txt4_3 <- vector()
for (i in seq(length(gene_id))) {
txt4_3 <- c(txt4_3, getGeneAnnotation(species01 = gene_specie[i], name01 = name_g[i], geneID01 = gene_id[i]))
}
txt4 <- c(txt4_1, txt4_2, txt4_3)
# merge the above file
txt_final0 <- c(txt1, txt2, txt30, txt4, txt5, txt7)
#----------------------------------------------------------
# txt6 Input the connection of metabolite into celldesigner
#---------------------------------------------------------
# input the common template
R3 <- readLines(file("data/txt6_repeated_part3")) # connect two parts
R5 <- readLines(file("data/txt6_repeated_part5.xml")) # mainly define connectScheme____version2
R7 <- readLines(file("data/txt6_repeated_part7")) # connect two parts
rxn <- rxn_core_carbon_inf
rxn_p0 <- gpr_inf
## change reaction into list format
## data process before using function
rxnID <- unique(rxn$rxnID)
rxn_annotation <- list()
rxn_id <- list()
for (i in 1:length(rxnID)) {
rxn_id[[i]] <- which(rxn$rxnID %in% rxnID[i] == TRUE)
rxn_annotation[[i]] <- rxn[rxn_id[[i]], ]
}
gpr0 <- list()
for (i in 1:length(rxn_p0$rxnID)) {
gpr0[[i]] <- rxn_p0[i, ]
}
## using the main function
txt6_new <- vector()
for (j in 1:length(rxnID)) {
txt6_new <- c(txt6_new, getRxnInformation(rxn_annotation[[j]], rxn_p = gpr0[[j]], R30=R3,R70=R7))
}
txt_new <- c(txt1, txt2, txt30, txt4, txt5, txt6_new, txt7) # connect each template
# save the file
# only with component coordinate
writeLines(txt_final0, file("result/model_add_metabolite_protein.xml")) # save
# adding the component connection
writeLines(txt_new, file("result/model_with_protein-add rxn connection.xml")) # save
}
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