## ----echo = F------------------------------------------------------------
library(MAGNAMWAR)
## ------------------------------------------------------------------------
lfrc_fasta <- system.file('extdata', 'RASTtoGBK//lfrc.fasta', package='MAGNAMWAR')
lfrc_reference <- system.file('extdata', 'RASTtoGBK//lfrc_lookup.csv', package='MAGNAMWAR')
lfrc_path <- system.file('extdata', 'RASTtoGBK//lfrc_out.fasta', package='MAGNAMWAR')
RASTtoGBK(lfrc_fasta,lfrc_reference,lfrc_path)
## ---- echo=FALSE---------------------------------------------------------
file_groups <- system.file('extdata', 'groups_example_r.txt', package='MAGNAMWAR')
## ---- results="hide"-----------------------------------------------------
# file_groups is the file path to your output file from OrthoMCL
parsed_data <- FormatAfterOrtho(file_groups, "groups")
## ---- echo = F-----------------------------------------------------------
parsed_data[[1]][,1:13]
## ---- echo = F-----------------------------------------------------------
parsed_data[[2]][,1:2]
## ---- echo = F-----------------------------------------------------------
head(pheno_data,n = 5)
## ---- results="hide"-----------------------------------------------------
mcl_matrix <- AnalyzeOrthoMCL(parsed_data,
pheno_data,
model = 'lmeR2nest',
species_name = 'Treatment',
resp = 'RespVar',
rndm1 = 'Experiment',
rndm2 = 'Vial')
## ---- echo=F-------------------------------------------------------------
mcl_matrix[,1:3]
## ---- echo=F-------------------------------------------------------------
starv_pheno_data[1:3,]
## ----eval=FALSE----------------------------------------------------------
# mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, starv_pheno_data, species_name = 'TRT', model='survmulti', time='t2', event='event', rndm1='EXP', rndm2='VIAL', multi=1)
## ------------------------------------------------------------------------
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
joined_matrix <- JoinRepSeq(after_ortho_format_grps, dir, mcl_mtrx_grps, fastaformat = 'old')
## ---- echo=F-------------------------------------------------------------
joined_matrix[1,8:10]
## ---- fig.width=8, fig.height=4------------------------------------------
PDGPlot(pheno_data, mcl_matrix, OG = 'ex_r00002', species_colname = 'Treatment', data_colname = 'RespVar', ylab = "TAG Content")
## ---- fig.width=8, fig.height=4------------------------------------------
tree <- system.file('extdata', 'muscle_tree2.dnd', package='MAGNAMWAR')
PDGPlot(pheno_data, mcl_matrix, 'ex_r00002', 'Treatment', 'RespVar', ylab = "TAG Content", tree = tree)
## ---- fig.width=6, fig.height=6.5, fig.align='center'--------------------
PhyDataError(tree, pheno_data, mcl_matrix, species_colname = 'Treatment', data_colname = 'RespVar', OG='ex_r00002', xlabel='TAG Content')
## ------------------------------------------------------------------------
PDGvOG(parsed_data,0)
## ---- fig.width=4, fig.height=4, fig.align='center'----------------------
QQPlotter(mcl_matrix)
## ---- fig.width=6, fig.height=3, fig.align='center'----------------------
ManhatGrp(parsed_data, mcl_matrix)
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