#' @name makePlotFamilies_1quadrant
#' @rdname makePlotFamilies_1quadrant
#' @title Make plot families in first quadrant.
#' @author April/Frederik
#' @family plot
#' @export
makePlotFamilies_1quadrant <- function(data_fam, data, sortPF){ #data_gna,
### replace logFC and pvalue in di* by these from dpm
data_fam$logFC <- data$logFC[match(data_fam$gene, data$gene)]
data_fam$pvalue <- data$pvalue[match(data_fam$gene, data$gene)]
if(sortPF == "sort_f"){
data_fam <- data_fam[order(-data_fam$frequency), ]
if(nrow(data_fam)>=1){
data_fam <- cbind(data_fam, new_f = paste0("(", data_fam$frequency, ") ", data_fam$overlay))
}
else {
data_fam <- data.frame("id" = character(0), "rep1" = numeric(0), "rep2" = numeric(0),
"logFC" = numeric(0), "pvalue" = numeric(0), "FDR" = numeric(0),
"gene" = character(0), "overlay" = character(0), "frequency" = numeric(0),
"new_f" = character(0))
}
}
else if(sortPF == "sort_a"){
data_fam
if(nrow(data_fam)>=1){
data_fam <- cbind(data_fam, new_f = paste0(data_fam$overlay, " (", data_fam$frequency, ")"))
}
else {
data_fam <- data.frame("id" = character(0), "rep1" = numeric(0), "rep2" = numeric(0),
"logFC" = numeric(0), "pvalue" = numeric(0), "FDR" = numeric(0),
"gene" = character(0), "overlay" = character(0), "frequency" = numeric(0),
"new_f" = character(0))
}
}
data_fam$new_f <- factor(data_fam$new_f, levels = unique(data_fam$new_f))
# data_gna$logFC <- data$logFC[match(data_gna$gene, data$gene)]
# data_gna$pvalue <- data$pvalue[match(data_gna$gene, data$gene)]
# pf_list <- list("list" = data_fam) #, "list" = data_gna
pf_list <- data_fam
pf_list
#for download
# families <- cbind(data_fam$gene, data_fam$family, data_fam$frequency)
# colnames(families) <- c("gene", "family", "frequency")
}
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