## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=TRUE, message=FALSE------------------------------------------------- #-- Libraries required in this section: #-- TreeAndLeaf(>=1.4.2), RedeR(>=1.40.4), Bioconductor >= 3.13 (R >= 4.0) # BiocManager::install(c("TreeAndLeaf","RedeR")) # install.packages(c("igraph","RColorBrewer")) #-- Load packages library("TreeAndLeaf") library("RedeR") library("igraph") library("RColorBrewer") ## ----eval=TRUE, message=FALSE------------------------------------------------- #-- Check data dim(USArrests) head(USArrests) ## ----eval=TRUE, message=FALSE------------------------------------------------- hc <- hclust(dist(USArrests), "ave") plot(hc, main="Dendrogram for the 'USArrests' dataset", xlab="", sub="") ## ----eval=FALSE--------------------------------------------------------------- # #-- Convert the 'hclust' object into a 'tree-and-leaf' object # tal <- treeAndLeaf(hc) ## ----eval=FALSE--------------------------------------------------------------- # #--- Map attributes to the tree-and-leaf # #Note: 'refcol = 0' indicates that 'dat' rownames will be used as mapping IDs # tal <- att.mapv(g = tal, dat = USArrests, refcol = 0) ## ----eval=FALSE--------------------------------------------------------------- # #--- Set graph attributes using the 'att.setv' wrapper function # pal <- brewer.pal(9, "Reds") # tal <- att.setv(g = tal, from = "Murder", to = "nodeColor", # cols = pal, nquant = 5) # tal <- att.setv(g = tal, from = "UrbanPop", to = "nodeSize", # xlim = c(10, 50, 5), nquant = 5) # # #--- Set graph attributes using 'att.addv' and 'att.adde' functions # tal <- att.addv(tal, "nodeFontSize", value = 15, index = V(tal)$isLeaf) # tal <- att.adde(tal, "edgeWidth", value = 3) ## ----eval=FALSE--------------------------------------------------------------- # #--- Call RedeR application # rdp <- RedPort() # calld(rdp) # resetd(rdp) ## ----eval=FALSE--------------------------------------------------------------- # #--- Send the tree-and-leaf to the interactive R/Java interface # addGraph(obj = rdp, g = tal, gzoom=75) # # #--- Call 'relax' to fine-tune the leaf nodes # relax(rdp, p1=25, p2=200, p3=5, p5=5, ps=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # #--- Add legends # addLegend.color(obj = rdp, tal, title = "Murder Rate", # position = "topright") # addLegend.size(obj = rdp, tal, title = "Urban Population Size", # position = "bottomright") ## ----eval=FALSE, message=FALSE------------------------------------------------ # #-- Libraries required in this section: # #-- TreeAndLeaf(>=1.4.2), RedeR(>=1.40.4), Bioconductor >= 3.13 (R >= 4.0) # # BiocManager::install(c("TreeAndLeaf","RedeR","ggtree)) # # install.packages(c("igraph","ape", "dendextend", "dplyr", # # "ggplot2", "RColorBrewer")) # # #-- Load packages # library("TreeAndLeaf") # library("RedeR") # library("igraph") # library("ape") # library("ggtree") # library("dendextend") # library("dplyr") # library("ggplot2") # library("RColorBrewer") ## ----eval=FALSE--------------------------------------------------------------- # #--- Generate a random phylo tree # phylo_tree <- rcoal(300) # # #--- Set groups and node sizes # group <- size <- dendextend::cutree(phylo_tree, 10) # group[] <- LETTERS[1:10][group] # size[] <- sample(size) # group.df <- data.frame(label=names(group), group=group, size=size) # phylo_tree <- dplyr::full_join(phylo_tree, group.df, by='label') # # #--- Generate a ggtree with 'daylight' layout # pal <- brewer.pal(10, "Set3") # ggt <- ggtree(phylo_tree, layout = 'daylight', branch.length='none') # # #--- Plot the ggtree # ggt + geom_tippoint(aes(color=group, size=size)) + # scale_color_manual(values=pal) + scale_y_reverse() ## ----eval=FALSE--------------------------------------------------------------- # #-- Convert the 'ggtree' object into a 'tree-and-leaf' object # tal <- treeAndLeaf(ggt) # # #--- Map attributes to the tree-and-leaf # #Note: 'refcol = 1' indicates that 'dat' col 1 will be used as mapping IDs # tal <- att.mapv(g = tal, dat = group.df, refcol = 1) # # #--- Set graph attributes using the 'att.setv' wrapper function # tal <- att.setv(g = tal, from = "group", to = "nodeColor", # cols = pal) # tal <- att.setv(g = tal, from = "size", to = "nodeSize", # xlim = c(10, 50, 5)) # # #--- Set graph attributes using 'att.addv' and 'att.adde' functions # tal <- att.addv(tal, "nodeFontSize", value = 1) # tal <- att.addv(tal, "nodeLineWidth", value = 0) # tal <- att.addv(tal, "nodeColor", value = "black", index=!V(tal)$isLeaf) # tal <- att.adde(tal, "edgeWidth", value = 3) # tal <- att.adde(tal, "edgeColor", value = "black") ## ----eval=FALSE--------------------------------------------------------------- # #--- Call RedeR application # rdp <- RedPort() # calld(rdp) # resetd(rdp) ## ----eval=FALSE--------------------------------------------------------------- # #--- Send the tree-and-leaf to the interactive R/Java interface # addGraph(obj = rdp, g = tal, gzoom=50) # # #--- Select inner nodes, preventing them from relaxing # selectNodes(rdp, V(tal)$name[!V(tal)$isLeaf], anchor=TRUE) # # #--- Call 'relax' to fine-tune the leaf nodes # relax(rdp, p1=25, p2=100, p3=5, p5=1, p8=5, ps=TRUE) # # #--- Add legends # addLegend.color(obj = rdp, tal, title = "Group", # position = "topright",vertical=T) # addLegend.size(obj = rdp, tal, title = "Size", # position = "topleft", # vertical=T, dxtitle=10) ## ----eval=FALSE, message=FALSE------------------------------------------------ # #-- Libraries required in this section: # #-- TreeAndLeaf(>=1.4.2), RedeR(>=1.40.4), Bioconductor >= 3.13 (R >= 4.0) # # BiocManager::install(c("TreeAndLeaf","RedeR")) # # install.packages(c("igraph", "RColorBrewer")) # # #-- Load packages # library(TreeAndLeaf) # library(RedeR) # library(igraph) # library(RColorBrewer) ## ----echo=TRUE---------------------------------------------------------------- #-- Check data dim(quakes) head(quakes) ## ----eval=TRUE, message=FALSE------------------------------------------------- #-- Building a large dendrogram hc <- hclust(dist(quakes), "ave") plot(hc, main="Dendrogram for the 'quakes' dataset", xlab="", sub="") ## ----eval=FALSE--------------------------------------------------------------- # #-- Convert the 'hclust' object into a 'tree-and-leaf' object # tal <- treeAndLeaf(hc) ## ----eval=FALSE--------------------------------------------------------------- # #--- Map attributes to the tree-and-leaf # #Note: 'refcol = 0' indicates that 'dat' rownames will be used as mapping IDs # tal <- att.mapv(tal, quakes, refcol = 0) # # #--- Set graph attributes using the 'att.setv' wrapper function # pal <- brewer.pal(9, "Greens") # tal <- att.setv(g = tal, from = "mag", to = "nodeColor", # cols = pal, nquant = 10) # tal <- att.setv(g = tal, from = "depth", to = "nodeSize", # xlim = c(40, 120, 20), nquant = 5) # # #--- Set graph attributes using 'att.addv' and 'att.adde' functions # tal <- att.addv(tal, "nodeFontSize", value = 1) # tal <- att.adde(tal, "edgeWidth", value = 10) ## ----eval=FALSE--------------------------------------------------------------- # #--- Call RedeR application # rdp <- RedPort() # calld(rdp) # resetd(rdp) ## ----eval=FALSE--------------------------------------------------------------- # #--- Send the tree-and-leaf to the interactive R/Java interface # addGraph(obj = rdp, g = tal, gzoom=10) # # #--- Call 'relax' to fine-tune the leaf nodes # relax(rdp, p1=25, p2=200, p3=10, p4=100, p5=10, ps=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # #--- Add legends # addLegend.color(obj = rdp, tal, title = "Richter Magnitude", # position = "bottomright") # addLegend.size(obj = rdp, tal, title = "Depth (km)") ## ----eval=TRUE, message=FALSE------------------------------------------------- #-- Libraries required in this section: #-- TreeAndLeaf(>=1.4.2), RedeR(>=1.40.4), Bioconductor >= 3.13 (R >= 4.0) # BiocManager::install(c("TreeAndLeaf","RedeR","geneplast)) # install.packages(c("igraph","ape", "RColorBrewer")) #-- Load packages library(TreeAndLeaf) library(RedeR) library(igraph) library(ape) library(geneplast) library(RColorBrewer) ## ----eval=TRUE, message=FALSE------------------------------------------------- #-- Load data and plot the phylogenetic tree data("spdata") data("gpdata.gs") plot(phyloTree) ## ----eval=FALSE--------------------------------------------------------------- # #--- Drop organisms not listed in the 'spdata' annotation # phyloTree$tip.label <- as.character(phyloTree$tip.label) # tokeep <- phyloTree$tip.label %in% spdata$tax_id # pruned.phylo <- drop.tip(phyloTree, phyloTree$tip.label[!tokeep]) ## ----eval=FALSE--------------------------------------------------------------- # #-- Convert the phylogenetic tree into a 'tree-and-leaf' object # tal <- treeAndLeaf(pruned.phylo) # # #--- Map attributes to the tree-and-leaf # #Note: 'refcol = 1' indicates that 'dat' col 1 will be used as mapping IDs # tal <- att.mapv(g = tal, dat = spdata, refcol = 1) # # #--- Set graph attributes using the 'att.setv' wrapper function # pal <- brewer.pal(9, "Purples") # tal <- att.setv(g = tal, from = "genome_size_Mb", # to = "nodeSize", xlim = c(120, 250, 1), nquant = 5) # tal <- att.setv (g = tal, from = "proteins", # to = "nodeColor", nquant = 5, # cols = pal, na.col = "black") ## ----eval=FALSE--------------------------------------------------------------- # #--- Add graph attributes using 'att.adde' and 'att.addv' functions # tal <- att.addv(tal, "nodeFontSize", value = 10) # tal <- att.adde(tal, "edgeWidth", value = 20) # # # Set species names to 'nodeAlias' attribute # tal <- att.setv(tal, from = "sp_name", to = "nodeAlias") # # # Select a few names to highlight in the graph # tal <- att.addv(tal, "nodeFontSize", value = 100, # filter=list('name'=sample(pruned.phylo$tip.label,30))) # tal <- att.addv(tal, "nodeFontSize", value = 100, # filter=list('name'="9606")) #Homo sapiens ## ----eval=FALSE--------------------------------------------------------------- # # Call RedeR # rdp <- RedPort() # calld(rdp) # resetd(rdp) # # #--- Send the tree-and-leaf to the interactive R/Java interface # addGraph(obj = rdp, g = tal, gzoom=10) # # #--- Call 'relax' to fine-tune the leaf nodes # relax(rdp, ps=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # #--- Add legends # addLegend.color(rdp, tal, title = "Proteome Size (n)") # addLegend.size(rdp, tal, title = "Genome Size (Mb)") ## ----eval=FALSE--------------------------------------------------------------- # #-- Libraries required in this section: # #-- TreeAndLeaf(>=1.4.2), RedeR(>=1.40.4), Bioconductor >= 3.13 (R >= 4.0) # # BiocManager::install(c("TreeAndLeaf","RedeR","geneplast)) # # install.packages(c("igraph","ape", "RColorBrewer")) # # #-- Load packages # library(TreeAndLeaf) # library(RedeR) # library(igraph) # library(ape) # library(geneplast) # library(RColorBrewer) ## ----eval=FALSE, message=FALSE------------------------------------------------ # #-- Load data # data("spdata") # data("phylo_tree") ## ----eval=FALSE, message=FALSE------------------------------------------------ # #--- Drop organisms not listed in the 'spdata' annotation # tokeep <- phylo_tree$tip.label %in% spdata$tax_id # pruned.phylo <- drop.tip(phylo_tree, phylo_tree$tip.label[!tokeep]) ## ----eval=FALSE--------------------------------------------------------------- # #-- Convert the phylogenetic tree into a 'tree-and-leaf' object # tal <- treeAndLeaf(pruned.phylo) ## ----eval=FALSE--------------------------------------------------------------- # #--- Map attributes to the tree-and-leaf using "%>%" operator # tal <- tal %>% # att.mapv(dat = spdata, refcol = 1) %>% # att.setv(from = "genome_size_Mb", to = "nodeSize", # xlim = c(120, 250, 1), nquant = 5) %>% # att.setv(from = "proteins", to = "nodeColor", nquant = 5, # cols = brewer.pal(9, "Blues"), na.col = "black") %>% # att.setv(from = "sp_name", to = "nodeAlias") %>% # att.adde(to = "edgeWidth", value = 20) %>% # att.addv(to = "nodeFontSize", value = 10) %>% # att.addv(to = "nodeFontSize", value = 100, # filter = list("name" = sample(pruned.phylo$tip.label, 30))) %>% # att.addv(to = "nodeFontSize", value = 100, # filter = list("name" = "9606")) ## ----eval=FALSE--------------------------------------------------------------- # # Call RedeR # rdp <- RedPort() # calld(rdp) # resetd(rdp) # # #--- Send the tree-and-leaf to the interactive R/Java interface # addGraph(obj = rdp, g = tal, gzoom=5) # # #--- Call 'relax' to fine-tune the leaf nodes # relax(rdp, ps=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # #--- Add legends # addLegend.color(rdp, tal, title = "Proteome Size (n)") # addLegend.size(rdp, tal, title = "Genome size (Mb)") ## ----label='Session information', eval=TRUE, echo=FALSE----------------------- sessionInfo()