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Commit c421bc17 authored by anna-pacinkova's avatar anna-pacinkova
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noPK adn TFtargs corr

parent c715128f
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...@@ -45,9 +45,9 @@ ...@@ -45,9 +45,9 @@
#' #'
#' @return List of 7 elements needed to plot the final regulatory network #' @return List of 7 elements needed to plot the final regulatory network
#' @export #' @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, OMICS_mod_res, edge_weights = "MCMC_freq", edge_freq_thres = NULL, gene_ID,
TFtargs) TFtargs = NULL)
{ {
if(!(edge_weights %in% c("MCMC_freq","empB"))) if(!(edge_weights %in% c("MCMC_freq","empB")))
{ {
...@@ -117,8 +117,12 @@ TFtargs) ...@@ -117,8 +117,12 @@ TFtargs)
y = strength_threshold+0.015, col="#E69F00") y = strength_threshold+0.015, col="#E69F00")
grDevices::dev.off() grDevices::dev.off()
PK <- PK[PK$src_entrez %in% unlist(lapply(OMICS_mod_res$omics,colnames)),] if(!is.null(PK))
PK <- PK[PK$dest_entrez %in% unlist(lapply(OMICS_mod_res$omics,colnames)),] {
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") if(gene_ID=="entrezID")
{ {
...@@ -233,8 +237,8 @@ normalise <- function (x, from = range(x), to = c(0, 1)) { ...@@ -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 #' @return List of 6 elements needed to plot the final regulatory network edges
#' @export #' @export
edge_types <- function(mcmc_res, PK, gene_annot, edge_list, node_list, edge_types <- function(mcmc_res, PK = NULL, gene_annot, edge_list, node_list,
OMICS_mod_res, edge_weights, TFtargs) OMICS_mod_res, edge_weights, TFtargs = NULL)
{ {
omics <- OMICS_mod_res$omics omics <- OMICS_mod_res$omics
layers_def <- OMICS_mod_res$layers_def layers_def <- OMICS_mod_res$layers_def
...@@ -242,35 +246,52 @@ OMICS_mod_res, edge_weights, TFtargs) ...@@ -242,35 +246,52 @@ OMICS_mod_res, edge_weights, TFtargs)
if(any(regexpr("ENTREZID:",node_list)>0)) 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") if(edge_weights=="empB")
{ {
edge_list[,"edge_type"] <- "empirical" edge_list[,"edge_type"] <- "empirical"
TF_pk <- as.matrix(TFtargs[intersect(edge_list[,"to"],
rownames(TFtargs)), intersect(edge_list[,"from"], if(!is.null(TFtargs))
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, TF_pk <- as.matrix(TFtargs[intersect(edge_list[,"to"],
arr.ind = TRUE)[,2]], rownames(TF_pk)[which(TF_pk==1, rownames(TFtargs)), intersect(edge_list[,"from"],
arr.ind = TRUE)[,1]], sep="_") colnames(TFtargs))])
edge_list[match(intersect(edge_list[,"edge"],TF_pk), colnames(TF_pk) <- intersect(edge_list[,"from"],
edge_list[,"edge"]),"edge_type"] <- "TF" colnames(TFtargs))
} # end if(ncol(TF_pk)>=1) if(ncol(TF_pk)>=1)
edge_list[match(intersect(edge_list[,"edge"],PK), {
edge_list[,"edge"]), "edge_type"] <- "PK" 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"] <- edge_list[,"weight"] <-
round(as.numeric(unlist(lapply(seq_along(edge_list[,2]), 1, round(as.numeric(unlist(lapply(seq_along(edge_list[,2]), 1,
FUN=function(row) FUN=function(row)
mcmc_res$B_prior_mat_weighted[edge_list[row,"from"], mcmc_res$B_prior_mat_weighted[edge_list[row,"from"],
edge_list[row,"to"]]))), 2) edge_list[row,"to"]]))), 2)
} else { } else {
edge_list[match(setdiff(edge_list[,"edge"],PK), if(!is.null(PK))
edge_list[,"edge"]),"edge_type"] <- "new" {
edge_list[match(intersect(edge_list[,"edge"],PK),edge_list[,"edge"]), edge_list[match(setdiff(edge_list[,"edge"],PK),
"edge_type"] <- "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") } # end if else (edge_weights=="empB")
ge_cols <- RColorBrewer::brewer.pal(9, "Blues") ge_cols <- RColorBrewer::brewer.pal(9, "Blues")
...@@ -444,16 +465,19 @@ OMICS_mod_res, edge_weights, TFtargs) ...@@ -444,16 +465,19 @@ OMICS_mod_res, edge_weights, TFtargs)
} # end if(any(mapply(omics,FUN=function(list)... } # end if(any(mapply(omics,FUN=function(list)...
} else { } else {
if(!is.null(PK))
PK_src_dest <- {
as.character(gene_annot$gene_symbol[match( PK_src_dest <- as.character(gene_annot$gene_symbol[match(
PK$src_entrez,gene_annot$entrezID)]) PK$src_entrez,gene_annot$entrezID)])
PK_src_dest[regexpr("entrezid",PK_src_dest)>0] <- tolower( PK_src_dest[regexpr("entrezid",PK_src_dest)>0] <- tolower(
as.character(gene_annot$gene_symbol[match(toupper(PK_src_dest[ as.character(gene_annot$gene_symbol[match(toupper(PK_src_dest[
regexpr("entrezid",PK_src_dest)>0]), gene_annot$entrezID)])) regexpr("entrezid",PK_src_dest)>0]), gene_annot$entrezID)]))
PK_src_dest[is.na(PK_src_dest)] <- PK$src_entrez[is.na(PK_src_dest)] PK_src_dest[is.na(PK_src_dest)] <-
PK <- paste(PK_src_dest, as.character(gene_annot$gene_symbol[ PK$src_entrez[is.na(PK_src_dest)]
match(PK$dest_entrez,gene_annot$entrezID)]), sep="_") PK <- paste(PK_src_dest, as.character(gene_annot$gene_symbol[
match(PK$dest_entrez,gene_annot$entrezID)]), sep="_")
} # end if(!is.null(PK))
if(edge_weights=="empB") if(edge_weights=="empB")
{ {
edge_list[,"edge_type"] <- "empirical" edge_list[,"edge_type"] <- "empirical"
...@@ -461,41 +485,52 @@ OMICS_mod_res, edge_weights, TFtargs) ...@@ -461,41 +485,52 @@ OMICS_mod_res, edge_weights, TFtargs)
gene_annot$gene_symbol)] gene_annot$gene_symbol)]
TFs_eid <- gene_annot$entrezID[match(edge_list[,"from"], TFs_eid <- gene_annot$entrezID[match(edge_list[,"from"],
gene_annot$gene_symbol, nomatch = 0)] gene_annot$gene_symbol, nomatch = 0)]
TF_pk <- as.matrix(TFtargs[intersect(targs_eid, rownames(TFtargs)), if(!is.null(TFtargs))
intersect(TFs_eid, colnames(TFtargs))])
colnames(TF_pk) <- intersect(TFs_eid, colnames(TFtargs))
if(ncol(TF_pk)>=1)
{ {
TF_pk <- paste(gene_annot$gene_symbol[match(colnames(TF_pk) TF_pk <- as.matrix(TFtargs[intersect(targs_eid, rownames(TFtargs)),
[which(TF_pk==1, arr.ind = TRUE)[,2]], intersect(TFs_eid, colnames(TFtargs))])
gene_annot$entrezID)], gene_annot$gene_symbol[match( colnames(TF_pk) <- intersect(TFs_eid, colnames(TFtargs))
rownames(TF_pk)[which(TF_pk==1, arr.ind = TRUE)[,1]], if(ncol(TF_pk)>=1)
gene_annot$entrezID)], sep="_") {
edge_list[match(intersect(edge_list[,"edge"],TF_pk), TF_pk <- paste(gene_annot$gene_symbol[match(colnames(TF_pk)
edge_list[,"edge"]),"edge_type"] <- "TF" [which(TF_pk==1, arr.ind = TRUE)[,2]],
} # end if(ncol(TF_pk)>=1) gene_annot$entrezID)], gene_annot$gene_symbol[match(
rownames(TF_pk)[which(TF_pk==1, arr.ind = TRUE)[,1]],
edge_list[match(intersect(edge_list[,"edge"],PK), gene_annot$entrezID)], sep="_")
edge_list[,"edge"]), "edge_type"] <- "PK" edge_list[match(intersect(edge_list[,"edge"],TF_pk),
rownames(mcmc_res$B_prior_mat_weighted)[!is.na(match(rownames( edge_list[,"edge"]),"edge_type"] <- "TF"
mcmc_res$B_prior_mat_weighted), gene_annot$entrezID))] <- } # end if(ncol(TF_pk)>=1)
gene_annot$gene_symbol[match(rownames( } # end if(!is.null(TFtargs))
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$entrezID))] <- if(!is.null(PK))
tolower(gene_annot$gene_symbol[match(toupper(rownames( {
mcmc_res$B_prior_mat_weighted)), gene_annot$entrezID, nomatch = 0)]) edge_list[match(intersect(edge_list[,"edge"],PK),
colnames(mcmc_res$B_prior_mat_weighted) <- edge_list[,"edge"]), "edge_type"] <- "PK"
rownames(mcmc_res$B_prior_mat_weighted) } # end if(!is.null(PK))
edge_list[,"weight"] <-
round(as.numeric(unlist(lapply(seq_along(edge_list[,2]), rownames(mcmc_res$B_prior_mat_weighted)[!is.na(match(rownames(
FUN=function(row) mcmc_res$B_prior_mat_weighted[ mcmc_res$B_prior_mat_weighted), gene_annot$entrezID))] <-
edge_list[row,"from"],edge_list[row,"to"]]))),2) 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 { } else {
edge_list[match(setdiff(edge_list[,"edge"],PK), if(!is.null(PK))
edge_list[,"edge"]),"edge_type"] <- "new" {
edge_list[match(intersect(edge_list[,"edge"],PK), edge_list[match(setdiff(edge_list[,"edge"],PK),
edge_list[,"edge"]), "edge_type"] <- "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") } # end if else (edge_weights=="empB")
ge_cols <- RColorBrewer::brewer.pal(9, "Blues") ge_cols <- RColorBrewer::brewer.pal(9, "Blues")
......
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