Commit a47c5da4 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

v2.0.0 release

parent 556acf47
......@@ -34,11 +34,12 @@ rogge_12231.conf config file. Parameters need to be set by the user inside this
rogge_12231_workflow.sh file allowing checkings and SLURM job submission
rogge_12231_main_analysis.R R script run by SLURM
rogge_12231_data_compilation.R R script run by SLURM that compil the data from the previous loops
The four files must be in the same directory before running
rogge_12231_manual_graph_adjustment.R optional R script to run in R, after SLURM job, to improve the representation of the graphs. Open the script and set the parameter inside before running
#### OUTPUT DESCRIPTION
#### TARS OUTPUT DESCRIPTION
## For each job submitted to SLURM:
workflow_log messages printed by the rogge_12231_workflow.sh script
......@@ -59,6 +60,11 @@ Check for updated versions (most recent tags) at https://gitlab.pasteur.fr/gmill
#### WHAT'S NEW IN
## v2.0.0
rogge_12231_manual_graph_adjustment.R file added
## v1.0.0
Everything
......
......@@ -638,7 +638,7 @@ if(nrow(final.mod.gene.names) == 0 | nrow(na.omit(final.mod.gene.names)) == 0){
}
print(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))
fun_export_data(path = path.out, data = paste0("SEE THE final.mod.gene.names AND THE final.mod.gene.names.freq OBJECTS IN THE compiled_data.RData FILE PRESENT IN: ", path.out), output = log.file)
backup.name <- c(backup.name, "final.mod.gene.names.freq")
backup.name <- c(backup.name, "final.mod.gene.names.freq", "optimal.gene.nb", "selected.gene.names")
}
......@@ -792,10 +792,9 @@ if(analysis.kind == "valid_boot"){
tempo <- dev.set(pdf.nb) # assign to avoid the message
corrplot::corrplot(cor(nano.rf.selected.genes), tl.col = "black", tl.cex = label.size / 10)
fun_export_data(path = path.out, data = paste0("SEE THE nano.rf.selected.genes OBJECTS IN THE compiled_data.RData FILE PRESENT IN: ", path.out), output = log.file)
backup.name <- c(backup.name, "nano.rf.selected.genes")
}
}
backup.name <- c(backup.name, "nano.rf.selected.genes", "dat")
######## 4.2 Validate the model
......@@ -837,6 +836,7 @@ for(i0 in 1:length(data.kind)){
for(i2 in 1:slurm.loop.nb){
# roc curves
if(nrow(get(paste0("loop", i2, "_data.roc", i0, ".", data.kind[i0], ".", ana.kind[i1]))) > 0){
backup.name <- c(backup.name, paste0("loop", i2, "_data.roc", i0, ".", data.kind[i0], ".", ana.kind[i1]))
assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_line(data = get(paste0("loop", i2, "_data.roc", i0, ".", data.kind[i0], ".", ana.kind[i1]))[order(get(paste0("loop", i2, "_data.roc", i0, ".", data.kind[i0], ".", ana.kind[i1]))$x, get(paste0("loop", i2, "_data.roc", i0, ".", data.kind[i0], ".", ana.kind[i1]))$y, decreasing = FALSE), ], mapping = ggplot2::aes(x = x, y = y), color = "grey", alpha = 0.5))
}
}
......@@ -891,6 +891,7 @@ boxdat <- data.frame(ASDAS = df.nano$response_ASDAS_R_NR,
)
boxdat_melt <- reshape2::melt(boxdat, id.vars = c("ASDAS", "Cohort.name", "RF.COHORTE"), variable.name = "Gene")
boxdat_melt$Gene <- factor(boxdat_melt$Gene, levels = unique(boxdat_melt$Gene))
backup.name <- c(backup.name, "boxdat_melt")
# boxplot
bar.width <- 0.5
......
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