## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  library(dowser)
#  library(ggtree)
#  # load example tsv data
#  data("ExampleMixedDb")
#  
#  # find the clone subgroups
#  ExampleMixedDb <- resolveLightChains(ExampleMixedDb)
#  print(ExampleMixedDb$clone_subgroup)

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  # run createGermlines -- this will create new germline for each locus in each subgroup
#  # the directory for the references matches the location on docker
#  references <- readIMGT("/usr/local/share/germlines/imgt/human/vdj")
#  ExampleMixedDb <- createGermlines(ExampleMixedDb, references = references, clone = "clone_subgroup_id", nproc = 1)

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  clones <- formatClones(ExampleMixedDb, chain="HL", nproc=1, collapse = FALSE,
#                         split_light = TRUE, minseq = 3)
#  print(clones)

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  # Building maximum likelihood trees with multiple partitions using IgPhyML
#  # Only the newest version of IgPhyML supports this option
#  # exec here is set to IgPhyML position in the Docker image.
#  clones <- getTrees(clones, build="igphyml", nproc=1, partition="hl",
#                     exec="/usr/local/share/igphyml/src/igphyml")

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  plotTrees(clones)[[1]]+geom_tiplab()+xlim(0,0.35)

## ----eval=TRUE, warning=FALSE, message=FALSE, echo=FALSE----------------------
library(dowser)
library(ggtree)
# Load data instead of running IgPhyML
data(ExampleMixedClones)

ExampleMixedClones$trees <- ExampleMixedClones$igphyml_partitioned_trees

plotTrees(ExampleMixedClones)[[1]] + geom_tiplab() +xlim(0,0.35)

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  
#  # exec is set to RAxML position in the Docker image.
#  clones = getTrees(clones, build="raxml",
#      exec="/usr/local/bin/raxml-ng", nproc=1, partition="scaled")

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
#  plotTrees(clones)[[1]]+geom_tiplab()+xlim(0, 0.12)

## ----eval=TRUE, warning=FALSE, message=FALSE, echo=FALSE----------------------
data(ExampleMixedClones)
# change the tree names
ExampleMixedClones$trees <- ExampleMixedClones$raxml_partitioned_trees
plotTrees(ExampleMixedClones)[[1]] + geom_tiplab() + xlim(0, 0.12)

