## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# library(dowser)
# 
# data(ExampleClones)
# 
# ExampleClones = ExampleClones[1:2,]
# 
# plots = plotTrees(ExampleClones)
# 
# #Plot the largest tree
# #To plot second largest tree, use plots[[2]], and so on
# plots[[1]]
# 

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# # Re-scale branches to represent mutations between nodes
# ExampleClones_m = scaleBranches(ExampleClones, edge_type="mutations")
# 
# # Plot, set scale bar to represent 10 mutations
# plots = plotTrees(ExampleClones_m, scale=10)
# 
# #Plot the largest tree
# plots[[1]]
# 

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# # Plot tree with sequence isotype at the tips.
# plots = plotTrees(ExampleClones, tips="c_call")
# 
# #Plot the largest tree
# plots[[1]]

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# # Plot tree with sequence isotype at the tips, with sizes set to number of duplicates
# plots = plotTrees(ExampleClones, tips="c_call", tipsize="duplicate_count")
# 
# #Plot the largest tree
# plots[[1]]

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# # These calls create the same plot:
# 
# # Plot tree with sequence isotype at the tips, with palette "Set1"
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2,
#     palette="Paired")
# 
# # or, specify a named palette vector
# custom_palette=c(
#     "IGHM"    ="#a6cee3",
#     "IGHD"    ="#1f78b4",
#     "IGHG3"   ="#b2df8a",
#     "IGHG1"   ="#33a02c",
#     "IGHA1"   ="#fb9a99",
#     "IGHG2"   ="#e31a1c",
#     "IGHG4"   ="#fdbf6f",
#     "IGHE"    ="#ff7f00",
#     "IGHA2"   ="#cab2d6",
#     "Germline"="#6a3d9a")
# 
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2,
#       palette=custom_palette)
# 
# # or, use the getPalette function to create a named palette vector
# custom_palette = getPalette(c("IGHM","IGHD","IGHG3","IGHG1","IGHA1",
#     "IGHG2","IGHG4","IGHE","IGHA2"), "Paired")
# 
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2,
#     palette=custom_palette)
# 
# #Plot the largest tree
# plots[[1]]

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# library(ggtree)
# 
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2)
# 
# #Plot the largest tree
# treeplot = plots[[1]] + geom_tiplab() +
#     geom_vline(xintercept=c(0.05,0.1,0.15,0.2,0.25),
#         linetype="dashed",color="grey") + xlim(0,0.3) +
#     ggtitle("Example B cell tree")
# 
# treeplot

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# library(ggtree)
# 
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2)
# 
# #Plot the largest tree
# treeplot = plots[[1]] + geom_tiplab(aes(label=c_call), offset = 0.02) +
#     geom_vline(xintercept=c(0.05,0.1,0.15,0.2,0.25),
#         linetype="dashed",color="grey") + xlim(0,0.3) +
#     ggtitle("Example B cell tree")
# 
# treeplot

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# library(ggtree)
# 
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2)
# 
# #Manually adjust all trees
# treeplots = lapply(plots, function(x)
#   x + geom_tiplab(aes(label=c_call), offset = 0.02) +
#     geom_vline(xintercept=c(0.05,0.1,0.15,0.2,0.25),
#         linetype="dashed",color="grey") + xlim(0,0.3) +
#     ggtitle("Example B cell tree")
#   )
# 
# # plot 2nd largest tree
# treeplots[[2]]

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# plots = plotTrees(ExampleClones, tips="c_call", tipsize=2)
# 
# # you can also pass arguments you would pass to grDevices::pdf, like width and height
# # here, we plot 4 trees per page (2 rows, 2 columns)
# treesToPDF(plots, file="trees.pdf", nrow=2, ncol=2)

