diff --git a/R/Evaluation_func.R b/R/Evaluation_func.R
index d4b42b2bb8eda93f2963315001680d090bc5c3af..01dd47a553bd17a192307229006e8dba656c9eb9 100644
--- a/R/Evaluation_func.R
+++ b/R/Evaluation_func.R
@@ -45,9 +45,9 @@
#'
#' @return List of 7 elements needed to plot the final regulatory network
#' @export
-trace_plots <- function(mcmc_res, burn_in, thin, figures_dir, gene_annot, PK,
+trace_plots <- function(mcmc_res, burn_in, thin, figures_dir, gene_annot, PK=NULL,
OMICS_mod_res, edge_weights = "MCMC_freq", edge_freq_thres = NULL, gene_ID,
-TFtargs)
+TFtargs = NULL)
{
if(!(edge_weights %in% c("MCMC_freq","empB")))
{
@@ -117,8 +117,12 @@ TFtargs)
y = strength_threshold+0.015, col="#E69F00")
grDevices::dev.off()
- PK <- PK[PK$src_entrez %in% unlist(lapply(OMICS_mod_res$omics,colnames)),]
- PK <- PK[PK$dest_entrez %in% unlist(lapply(OMICS_mod_res$omics,colnames)),]
+ if(!is.null(PK))
+ {
+ PK <- PK[PK$src_entrez %in% unlist(lapply(OMICS_mod_res$omics,colnames)),]
+ PK <- PK[PK$dest_entrez %in% unlist(lapply(OMICS_mod_res$omics,colnames)),]
+ }
+
if(gene_ID=="entrezID")
{
@@ -233,8 +237,8 @@ normalise <- function (x, from = range(x), to = c(0, 1)) {
#'
#' @return List of 6 elements needed to plot the final regulatory network edges
#' @export
-edge_types <- function(mcmc_res, PK, gene_annot, edge_list, node_list,
-OMICS_mod_res, edge_weights, TFtargs)
+edge_types <- function(mcmc_res, PK = NULL, gene_annot, edge_list, node_list,
+OMICS_mod_res, edge_weights, TFtargs = NULL)
{
omics <- OMICS_mod_res$omics
layers_def <- OMICS_mod_res$layers_def
@@ -242,35 +246,52 @@ OMICS_mod_res, edge_weights, TFtargs)
if(any(regexpr("ENTREZID:",node_list)>0))
{
- PK <- paste(PK$src_entrez, PK$dest_entrez, sep="_")
-
+ if(!is.null(PK))
+ {
+ PK <- paste(PK$src_entrez, PK$dest_entrez, sep="_")
+ } # end if(!is.null(PK))
+
if(edge_weights=="empB")
{
edge_list[,"edge_type"] <- "empirical"
- TF_pk <- as.matrix(TFtargs[intersect(edge_list[,"to"],
- rownames(TFtargs)), intersect(edge_list[,"from"],
- colnames(TFtargs))])
- colnames(TF_pk) <- intersect(edge_list[,"from"], colnames(TFtargs))
- if(ncol(TF_pk)>=1)
+
+ if(!is.null(TFtargs))
{
- TF_pk <- paste(colnames(TF_pk)[which(TF_pk==1,
- arr.ind = TRUE)[,2]], rownames(TF_pk)[which(TF_pk==1,
- arr.ind = TRUE)[,1]], sep="_")
- edge_list[match(intersect(edge_list[,"edge"],TF_pk),
- edge_list[,"edge"]),"edge_type"] <- "TF"
- } # end if(ncol(TF_pk)>=1)
- edge_list[match(intersect(edge_list[,"edge"],PK),
- edge_list[,"edge"]), "edge_type"] <- "PK"
+ TF_pk <- as.matrix(TFtargs[intersect(edge_list[,"to"],
+ rownames(TFtargs)), intersect(edge_list[,"from"],
+ colnames(TFtargs))])
+ colnames(TF_pk) <- intersect(edge_list[,"from"],
+ colnames(TFtargs))
+ if(ncol(TF_pk)>=1)
+ {
+ TF_pk <- paste(colnames(TF_pk)[which(TF_pk==1,
+ arr.ind = TRUE)[,2]], rownames(TF_pk)[which(TF_pk==1,
+ arr.ind = TRUE)[,1]], sep="_")
+ edge_list[match(intersect(edge_list[,"edge"],TF_pk),
+ edge_list[,"edge"]),"edge_type"] <- "TF"
+ } # end if(ncol(TF_pk)>=1)
+ } # end if(!is.null(TFtargs))
+
+ if(!is.null(PK))
+ {
+ edge_list[match(intersect(edge_list[,"edge"],PK),
+ edge_list[,"edge"]), "edge_type"] <- "PK"
+ } # end if(!is.null(PK))
+
edge_list[,"weight"] <-
round(as.numeric(unlist(lapply(seq_along(edge_list[,2]), 1,
FUN=function(row)
mcmc_res$B_prior_mat_weighted[edge_list[row,"from"],
edge_list[row,"to"]]))), 2)
} else {
- edge_list[match(setdiff(edge_list[,"edge"],PK),
- edge_list[,"edge"]),"edge_type"] <- "new"
- edge_list[match(intersect(edge_list[,"edge"],PK),edge_list[,"edge"]),
- "edge_type"] <- "PK"
+ if(!is.null(PK))
+ {
+ edge_list[match(setdiff(edge_list[,"edge"],PK),
+ edge_list[,"edge"]),"edge_type"] <- "new"
+ edge_list[match(intersect(edge_list[,"edge"],PK),
+ edge_list[,"edge"]), "edge_type"] <- "PK"
+ } # end if(!is.null(PK))
+
} # end if else (edge_weights=="empB")
ge_cols <- RColorBrewer::brewer.pal(9, "Blues")
@@ -444,16 +465,19 @@ OMICS_mod_res, edge_weights, TFtargs)
} # end if(any(mapply(omics,FUN=function(list)...
} else {
-
- PK_src_dest <-
- as.character(gene_annot$gene_symbol[match(
- PK$src_entrez,gene_annot$entrezID)])
- PK_src_dest[regexpr("entrezid",PK_src_dest)>0] <- tolower(
- as.character(gene_annot$gene_symbol[match(toupper(PK_src_dest[
- regexpr("entrezid",PK_src_dest)>0]), gene_annot$entrezID)]))
- PK_src_dest[is.na(PK_src_dest)] <- PK$src_entrez[is.na(PK_src_dest)]
- PK <- paste(PK_src_dest, as.character(gene_annot$gene_symbol[
- match(PK$dest_entrez,gene_annot$entrezID)]), sep="_")
+ if(!is.null(PK))
+ {
+ PK_src_dest <- as.character(gene_annot$gene_symbol[match(
+ PK$src_entrez,gene_annot$entrezID)])
+ PK_src_dest[regexpr("entrezid",PK_src_dest)>0] <- tolower(
+ as.character(gene_annot$gene_symbol[match(toupper(PK_src_dest[
+ regexpr("entrezid",PK_src_dest)>0]), gene_annot$entrezID)]))
+ PK_src_dest[is.na(PK_src_dest)] <-
+ PK$src_entrez[is.na(PK_src_dest)]
+ PK <- paste(PK_src_dest, as.character(gene_annot$gene_symbol[
+ match(PK$dest_entrez,gene_annot$entrezID)]), sep="_")
+ } # end if(!is.null(PK))
+
if(edge_weights=="empB")
{
edge_list[,"edge_type"] <- "empirical"
@@ -461,41 +485,52 @@ OMICS_mod_res, edge_weights, TFtargs)
gene_annot$gene_symbol)]
TFs_eid <- gene_annot$entrezID[match(edge_list[,"from"],
gene_annot$gene_symbol, nomatch = 0)]
- TF_pk <- as.matrix(TFtargs[intersect(targs_eid, rownames(TFtargs)),
- intersect(TFs_eid, colnames(TFtargs))])
- colnames(TF_pk) <- intersect(TFs_eid, colnames(TFtargs))
- if(ncol(TF_pk)>=1)
+ if(!is.null(TFtargs))
{
- TF_pk <- paste(gene_annot$gene_symbol[match(colnames(TF_pk)
- [which(TF_pk==1, arr.ind = TRUE)[,2]],
- gene_annot$entrezID)], gene_annot$gene_symbol[match(
- rownames(TF_pk)[which(TF_pk==1, arr.ind = TRUE)[,1]],
- gene_annot$entrezID)], sep="_")
- edge_list[match(intersect(edge_list[,"edge"],TF_pk),
- edge_list[,"edge"]),"edge_type"] <- "TF"
- } # end if(ncol(TF_pk)>=1)
-
- edge_list[match(intersect(edge_list[,"edge"],PK),
- edge_list[,"edge"]), "edge_type"] <- "PK"
- rownames(mcmc_res$B_prior_mat_weighted)[!is.na(match(rownames(
- mcmc_res$B_prior_mat_weighted), gene_annot$entrezID))] <-
- gene_annot$gene_symbol[match(rownames(
- mcmc_res$B_prior_mat_weighted), gene_annot$entrezID, nomatch = 0)]
- rownames(mcmc_res$B_prior_mat_weighted)[!is.na(match(toupper(
- rownames(mcmc_res$B_prior_mat_weighted)), gene_annot$entrezID))] <-
- tolower(gene_annot$gene_symbol[match(toupper(rownames(
- mcmc_res$B_prior_mat_weighted)), gene_annot$entrezID, nomatch = 0)])
- colnames(mcmc_res$B_prior_mat_weighted) <-
- rownames(mcmc_res$B_prior_mat_weighted)
- edge_list[,"weight"] <-
- round(as.numeric(unlist(lapply(seq_along(edge_list[,2]),
- FUN=function(row) mcmc_res$B_prior_mat_weighted[
- edge_list[row,"from"],edge_list[row,"to"]]))),2)
+ TF_pk <- as.matrix(TFtargs[intersect(targs_eid, rownames(TFtargs)),
+ intersect(TFs_eid, colnames(TFtargs))])
+ colnames(TF_pk) <- intersect(TFs_eid, colnames(TFtargs))
+ if(ncol(TF_pk)>=1)
+ {
+ TF_pk <- paste(gene_annot$gene_symbol[match(colnames(TF_pk)
+ [which(TF_pk==1, arr.ind = TRUE)[,2]],
+ gene_annot$entrezID)], gene_annot$gene_symbol[match(
+ rownames(TF_pk)[which(TF_pk==1, arr.ind = TRUE)[,1]],
+ gene_annot$entrezID)], sep="_")
+ edge_list[match(intersect(edge_list[,"edge"],TF_pk),
+ edge_list[,"edge"]),"edge_type"] <- "TF"
+ } # end if(ncol(TF_pk)>=1)
+ } # end if(!is.null(TFtargs))
+
+
+ if(!is.null(PK))
+ {
+ edge_list[match(intersect(edge_list[,"edge"],PK),
+ edge_list[,"edge"]), "edge_type"] <- "PK"
+ } # end if(!is.null(PK))
+
+ rownames(mcmc_res$B_prior_mat_weighted)[!is.na(match(rownames(
+ mcmc_res$B_prior_mat_weighted), gene_annot$entrezID))] <-
+ gene_annot$gene_symbol[match(rownames(
+ mcmc_res$B_prior_mat_weighted), gene_annot$entrezID, nomatch = 0)]
+ rownames(mcmc_res$B_prior_mat_weighted)[!is.na(match(toupper(
+ rownames(mcmc_res$B_prior_mat_weighted)), gene_annot$entrezID))] <-
+ tolower(gene_annot$gene_symbol[match(toupper(rownames(
+ mcmc_res$B_prior_mat_weighted)), gene_annot$entrezID, nomatch = 0)])
+ colnames(mcmc_res$B_prior_mat_weighted) <-
+ rownames(mcmc_res$B_prior_mat_weighted)
+ edge_list[,"weight"] <-
+ round(as.numeric(unlist(lapply(seq_along(edge_list[,2]),
+ FUN=function(row) mcmc_res$B_prior_mat_weighted[
+ edge_list[row,"from"],edge_list[row,"to"]]))),2)
} else {
- edge_list[match(setdiff(edge_list[,"edge"],PK),
- edge_list[,"edge"]),"edge_type"] <- "new"
- edge_list[match(intersect(edge_list[,"edge"],PK),
- edge_list[,"edge"]), "edge_type"] <- "PK"
+ if(!is.null(PK))
+ {
+ edge_list[match(setdiff(edge_list[,"edge"],PK),
+ edge_list[,"edge"]),"edge_type"] <- "new"
+ edge_list[match(intersect(edge_list[,"edge"],PK),
+ edge_list[,"edge"]), "edge_type"] <- "PK"
+ } # end if(!is.null(PK))
} # end if else (edge_weights=="empB")
ge_cols <- RColorBrewer::brewer.pal(9, "Blues")