From b4ee6dfbf83d016dca09440cf5130d8938607c53 Mon Sep 17 00:00:00 2001
From: noriakis <nori@hgc.jp>
Date: Wed, 25 Oct 2023 09:47:04 +0900
Subject: [PATCH] setTree

---
 NAMESPACE           |  1 +
 R/plotCirclize.R    | 11 +++++++----
 R/utils.R           | 12 ++++++++++++
 man/plotCirclize.Rd |  3 +++
 man/setTree.Rd      | 21 +++++++++++++++++++++
 5 files changed, 44 insertions(+), 4 deletions(-)
 create mode 100644 man/setTree.Rd

diff --git a/NAMESPACE b/NAMESPACE
index df42d71..c487e94 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -32,6 +32,7 @@ export(plotKEGGPathway)
 export(plotPCA)
 export(plotTree)
 export(setAnnotation)
+export(setTree)
 export(strainClusterHeatmap)
 export(summariseAbundance)
 import(BiocFileCache)
diff --git a/R/plotCirclize.R b/R/plotCirclize.R
index 660db03..83061bd 100644
--- a/R/plotCirclize.R
+++ b/R/plotCirclize.R
@@ -21,6 +21,7 @@
 #' @param returnRawDf return the raw data frame used in the plot
 #' @param featCircos which type of circos to use in the corresponding feature
 #' @param include_gene include these gene IDs, ignoring the thesh_snp_gene argument
+#' @param only_genome_id show only the genome IDs
 #' @importFrom circlize CELL_META circos.clear circos.par circos.initialize circos.rect circos.barplot circos.track circos.text circos.points
 #' @return draw circlize plot
 #' @export
@@ -30,7 +31,7 @@ plotCirclize <- function(stana, candSp, genomeId, include_gene=NULL,
                          cols=c("tomato","steelblue","gold","seagreen"),
                          controlColor="steelblue", MAF=FALSE, cl=NULL,
                          featCircos=list(), showGeneName=TRUE,
-                         returnRawDf=FALSE,
+                         returnRawDf=FALSE, only_genome_id=FALSE,
                          featThresh=0, cex=0.3, textCex=0.5,bar_width=10,
                          contPalette=c("steelblue",
                           "tomato"), discPalette="Dark2") {
@@ -76,16 +77,18 @@ plotCirclize <- function(stana, candSp, genomeId, include_gene=NULL,
     qqcat("Genome ID in SNV information:\n")
     for (i in unique(info$genome_id)) {
       tmp_info <- subset(info, genome_id==i)
-      qqcat("  @{i}: @{min(tmp_info$position)} - @{max(tmp_info$position)}, number of position: @{nrow(tmp_info)}\n")
+      qqcat("  @{i}: @{min(tmp_info$position)} - @{max(tmp_info$position)}",
+      	", number of position: @{nrow(tmp_info)}\n")
     }
     
+    if (only_genome_id) {return(1)}
+    
     qqcat("Genome ID: @{genomeId}\n")
 
     ## Deleting "None" and gene ids with only one position
     info$genome_id <- info$genome_id |> strsplit("_") |> 
                                         vapply("[", 1, FUN.VALUE="character")
     circ_plot <- subset(info, info$genome_id==genomeId)
-
     if (length(featList)>0) {
       for (nm in names(featList)) {
           circ_plot[[nm]] <- featList[[nm]][row.names(circ_plot)]
@@ -99,9 +102,9 @@ plotCirclize <- function(stana, candSp, genomeId, include_gene=NULL,
       circ_plot <- subset(circ_plot, !circ_plot$gene_id %in% names(gene_num[gene_num<thresh_snp_gene]))
     } else {
       circ_plot <- subset(circ_plot, circ_plot$gene_id %in% include_gene)
-
     }
     qqcat("Included position: @{dim(circ_plot)[1]}\n")
+    if (dim(circ_plot)[1]==0) {stop("No position available, finishing ...")}
     if (returnRawDf) {return(circ_plot)}
     circos.clear() ## If have one
     circos.par(cell.padding=c(0.02,0,0.02,0),
diff --git a/R/utils.R b/R/utils.R
index 57c476c..6ce4d65 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -6,4 +6,16 @@
 cnDiscretize <- function(stana, species, cutoff=0.35) {
 	df <- stana@genes[["100224"]]
 	apply(df, 2, function(x) ifelse(x>cutoff, 1, 0)) |> data.frame()
+}
+
+#' setTree
+#' @param stana stana object
+#' @param species species ID
+#' @param tre tree to be set
+#' @export
+#' @return stana
+setTree <- function(stana, species, tre) {
+	if (class(tre)!="phylo") {stop("Please provide phylo object")}
+	stana@treeList[[species]] <- tre
+	return(stana)
 }
\ No newline at end of file
diff --git a/man/plotCirclize.Rd b/man/plotCirclize.Rd
index 0ee2069..9196cd3 100644
--- a/man/plotCirclize.Rd
+++ b/man/plotCirclize.Rd
@@ -18,6 +18,7 @@ plotCirclize(
   featCircos = list(),
   showGeneName = TRUE,
   returnRawDf = FALSE,
+  only_genome_id = FALSE,
   featThresh = 0,
   cex = 0.3,
   textCex = 0.5,
@@ -53,6 +54,8 @@ plotCirclize(
 
 \item{returnRawDf}{return the raw data frame used in the plot}
 
+\item{only_genome_id}{show only the genome IDs}
+
 \item{featThresh}{for numeric features, the values above this value will be colored , default to zero.}
 
 \item{cex}{point size}
diff --git a/man/setTree.Rd b/man/setTree.Rd
new file mode 100644
index 0000000..aaf2da8
--- /dev/null
+++ b/man/setTree.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{setTree}
+\alias{setTree}
+\title{setTree}
+\usage{
+setTree(stana, species, tre)
+}
+\arguments{
+\item{stana}{stana object}
+
+\item{species}{species ID}
+
+\item{tre}{tree to be set}
+}
+\value{
+stana
+}
+\description{
+setTree
+}