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thym.py
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thym.py
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import os
import rpy2.robjects as robjects
import json
def analysisTHYM(idxAnalysis, file_miRNA, file_RNA, pvalue, foldchange, contrasts, geneSelected):
root = "datasetTCGA" + os.sep + "THYM" + os.sep
path_file_miRNA = root + "miRNASeq" + os.sep + file_miRNA
path_file_RNA = root + "RNASeq" + os.sep + file_RNA
name_file_rdata = "static/tempAnalysis" + os.sep + "THYM_workspace.RData"
name_file_json = "static/tempAnalysis" + os.sep + "THYM_" + pvalue + "_" + foldchange + "_" + contrasts + ".json"
name_file_heatmap = "static/tempAnalysis" + os.sep + "THYM_" + pvalue + "_" + foldchange + "_" + contrasts + "_heatmap.jpg"
name_file_boxplot = "static/tempAnalysis" + os.sep + "THYM_" + pvalue + "_" + foldchange + "_" + contrasts + "_" + geneSelected + "_boxplot.jpg"
name_file_mithril_1 = "static/tempAnalysis" + os.sep + "input_mithril_THYM_" + contrasts
name_file_mithril_2 = "static/tempAnalysis" + os.sep + "input_mithril_THYM_" + contrasts + ".txt" #questo è per i contrasti che non sono ALL
robjects.r('''
library("limma")
library("Biobase")
library("gplots")
library("data.table")
library("jsonlite")
if({0} == 4) {{ #Creazione File di input per mithril
load(file="{3}")
if({4} == 0) {{
for (i in 1:5) {{
name.file <- paste(paste("{11}", i, sep="_"), ".txt", sep="")
write.table(results[i], name.file, sep="\t" ,row.names=TRUE, col.names = FALSE, quote = FALSE)
}}
}} else {{
write.table(results[1], "{12}", sep="\t" ,row.names=TRUE, col.names = FALSE, quote = FALSE)
}}
}} else if({0} == 3) {{ #Creazione boxplot per singolo gene
load(file="{3}")
gene <- "{9}"
exp.values <- as.vector(normalized.expressions$E[gene, rownames(df.patient)])
boxplot.data <- data.frame(Sample.Category=df.patient$masaoka_stage, Sample.Value=exp.values, row.names=rownames(df.patient))
jpeg(file="{10}")
boxplot(Sample.Value~Sample.Category, data=boxplot.data, main=paste0("Evaluation of ", gene), xlab="Sample Category", ylab="Expression Value")
dev.off()
}} else {{
if({0} == 1) {{ #Analisi per l'estrazione dei biomarcatori
# =========== LOAD BIOSPECIMEN CLINICAL ===========
col.df.1 <- c("bcr_patient_uuid","bcr_patient_barcode","tumor_status","masaoka_stage","histologic_diagnosis","gender","vital_status")
df.patient <- read.table("datasetTCGA/THYM/BiospecimenClinicalData/nationwidechildrens.org_clinical_patient_thym.txt", header=T, sep="\t")[col.df.1]
df.patient <- df.patient[-c(1,2),]
# =========== LOAD miRNA Seq ===========
df.miRNA <- read.table("{1}", header = T, sep = "\t", check.names=FALSE, row.names = 1)
df.miRNA <- data.matrix(df.miRNA[-1, seq(from=2, to=ncol(df.miRNA), by=2)])
# =========== LOAD RNA Seq ===========
df.RNA <- read.table("{2}", header = T, sep = "\t", check.names=FALSE, row.names = 1)
df.RNA <- data.matrix(df.RNA)
# =========== INTEGRATION DATA ===========
rownames(df.patient) <- as.vector(df.patient$bcr_patient_barcode)
df.patient <- df.patient[-which(df.patient$masaoka_stage == "[Not Available]"),] #Rimuovo tutti i levels '[Not Available]'
df.patient$masaoka_stage <- droplevels(df.patient)$masaoka_stage #rimuovo i livelli non utilizzati
col.patient.barcode <- as.vector(unique(df.patient$bcr_patient_barcode))
idx.col.miRNA <- array(unlist(lapply(col.patient.barcode, function(x) which(colnames(df.miRNA) %like% as.character(x)))))
idx.col.RNA <- array(unlist(lapply(col.patient.barcode, function(x) which(colnames(df.RNA) %like% as.character(x)))))
df.miRNA <- as.data.frame(df.miRNA[, idx.col.miRNA])
names(df.miRNA) <- substr(names(df.miRNA), -1, 12)
df.RNA <- as.data.frame(df.RNA[, idx.col.RNA])
names(df.RNA) <- substr(names(df.RNA), -1, 12)
col.union <- intersect(colnames(df.RNA), colnames(df.miRNA))
df.union <- data.matrix(rbind(df.miRNA[,col.union], df.RNA[,col.union]))
df.patient <- df.patient[match(colnames(df.union), df.patient$bcr_patient_barcode), ]
design.original <- model.matrix(~0+masaoka_stage, data=df.patient)
colnames(design.original) <- c("S1", "S2a", "S2b", "S3", "S4a","S4b")
# =========== ANALYSIS ===========
normalized.expressions <- voom(df.union, design.original)
initial.model <- lmFit(normalized.expressions, design.original)
limma.model <- eBayes(initial.model)
#ogni volta usate lo stadio precedente come controllo per vedere quali geni differiscono
contrasts <- makeContrasts(S2a-S1, S2b-S2a, S3-S2b, S4a-S3, S4b-S4a, levels=design.original)
contrasts.model <- eBayes(contrasts.fit(limma.model, contrasts))
}} else if({0} == 2) {{ #Analisi per l'estrazione dei biomarcatori (Custom)
load(file="{3}")
}}
if({4} == 0) {{
results <- topTableF(contrasts.model, number=nrow(df.union), adjust.method="BH", p.value={5}, lfc={6})
}} else {{
results <- topTable(contrasts.model, coef={4}, number=nrow(df.union), adjust.method="BH", p.value={5}, lfc={6})
}}
#print(nrow(results))
if(is.data.frame(results) && nrow(results)!=0) {{
json <- toJSON(results, pretty = T)
#cat(x) #serve a stamparlo
write(json, "{7}")
if(nrow(results) > 1) {{ #evito di stampare la heatmap, se il dataframe result è composto di una sola riga
de.genes <- rownames(results)
#de.expressions <- normalized.expressions$E[de.genes,]
de.expressions <- matrix(as.numeric(unlist(normalized.expressions$E[de.genes,])), nrow=nrow(normalized.expressions$E[de.genes,]))
jpeg(file="{8}")
heatmap.2(de.expressions, col=redgreen(100), scale="row", key=TRUE, symkey=FALSE, density.info="none", trace="none")
dev.off()
}}
}}
save.image(file="{3}")
}}
'''.format(idxAnalysis, path_file_miRNA, path_file_RNA, name_file_rdata, contrasts, pvalue,
foldchange, name_file_json, name_file_heatmap, geneSelected, name_file_boxplot, name_file_mithril_1, name_file_mithril_2))
nGenes = 0
if os.path.isfile(name_file_json) and (idxAnalysis == "1" or idxAnalysis == "2"):
#apro il json appena creato
with open(name_file_json, 'r') as f:
datastore = json.load(f)
htmlGenes = '<option value="">Seleziona...</option>'
htmlAllGenes = ''
for idx,value in enumerate(datastore):
htmlGenes += '<option value="'+value['_row']+'">'+value['_row']+'</option>'
htmlAllGenes += value['_row']+"<br />"
nGenes += 1
# questo html, mi serve per inserirlo nella lista dei geni
return htmlGenes, htmlAllGenes, nGenes, 0
elif idxAnalysis == "3" or idxAnalysis == "4": #è importante questa condizione, perchè allora causerà un errore sulla creazione del boxplot o nell'estrazione dei file di input
return '', '', nGenes, 0
return '', '', nGenes, 1