## ----pre-firstchunk1, echo=TRUE , eval=FALSE , results="hide" , message=FALSE , warning=FALSE----
## #Given a LowMACA object 'lm'
## lm <- newLowMACA(genes=c("TP53" , "TP63" , "TP73"))
## lmParams(lm)$clustal_cmd <- "/your/path/to/clustalo"


## ----pre-firstchunk2, echo=TRUE , eval=FALSE , results="hide" , message=FALSE , warning=FALSE----
## # Needed only on Windows - run once per R session
## # Adjust the path to match your installation of Ghostscript
## if(Sys.info()['sysname']=="Windows")
##   Sys.setenv(R_GSCMD = '"C:/Program Files/gs/gs9.15/bin/gswin64c.exe"')


## ----firstchunk, echo=TRUE , eval=TRUE,results="hide" , message=FALSE , warning=FALSE----
library(LowMACA)
#User Input
Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
        ,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
        ,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
    	  ,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
			  ,"HOXD3","ISL1","ISX","LHX8")
Pfam <- "PF00046"

## ----secondchunk, echo=TRUE----------------------------------------------
#Construct the object
lm <- newLowMACA(genes=Genes, pfam=Pfam)
str(lm , max.level=3)


## ----thirdchunk, echo=TRUE-----------------------------------------------
#See default parameters
lmParams(lm)
#Change some parameters
#Accept sequences even with no mutations
lmParams(lm)$min_mutation_number <- 0
#Changing selected tumor types
#Check the available tumor types in cBioPortal
available_tumor_types <- showTumorType()
head(available_tumor_types)
#Select melanoma, stomach adenocarcinoma, uterine cancer, lung adenocarcinoma, 
#lung squamous cell carcinoma, colon rectum adenocarcinoma and breast cancer
lmParams(lm)$tumor_type <- c("skcm" , "stad" , "ucec" , "luad" , "lusc" , "coadread" , "brca")


## ----fourthchunk, echo=TRUE , eval=TRUE----------------------------------
lm <- alignSequences(lm)


## ----fourthchunkBis, echo=TRUE , eval=TRUE  , message=FALSE , warning=FALSE----
lm <- alignSequences(lm , mail="lowmaca@gmail.com")


## ----fifthchunck, echo=TRUE, eval=TRUE-----------------------------------
str(lmAlignment(lm) , max.level=2 , vec.len=2)


## ----sixthchunk, echo=TRUE , eval=TRUE-----------------------------------
lm <- getMutations(lm)
lm <- mapMutations(lm)


## ----seventhchunk2, echo=TRUE,eval=TRUE----------------------------------
str(lmMutations(lm) , vec.len=3 , max.level=1)


## ----seventhchunk, echo=TRUE,eval=TRUE-----------------------------------
myMutationFreqs <- lmMutations(lm)$freq
#Showing the first genes
myMutationFreqs[ , 1:10]


## ----eighthchunk, echo=TRUE , eval=FALSE , message=FALSE , warning=FALSE----
## #Local Installation of clustalo
## lm <- setup(lm)
## #Web Service
## lm <- setup(lm , mail="lowmaca@gmail.com")


## ----ninthchunk, echo=TRUE-----------------------------------------------
str(lmMutations(lm)$data , vec.len=1)


## ----tenthchunk, echo=TRUE , eval=TRUE-----------------------------------
lm <- entropy(lm)
#Global Score
str(lmEntropy(lm))
#Per position score
head(lmAlignment(lm)$df)


## ----eleventhchunk, echo=TRUE--------------------------------------------
significant_muts <- lfm(lm)
#Display original mutations that formed significant clusters (column Multiple_Aln_pos)
head(significant_muts)
#What are the genes mutated in position 4 in the consensus?
cluster_4_genes <- significant_muts[ significant_muts$Multiple_Aln_pos==4 , 'Gene_Symbol']

## ----eleventh_2chunck , echo=TRUE----------------------------------------
sort(table(cluster_4_genes))


## ----echo=TRUE, eval=TRUE, results="hide"--------------------------------
bpAll(lm)


## ----echo=TRUE, eval=TRUE, results="hide"--------------------------------
lmPlot(lm)


## ----protterChunk, echo=TRUE, eval=TRUE ,message=FALSE ,warning=FALSE----
#This plot is saved as a png image
protter(lm , filename="homeobox.png")

## ----protterremover, echo=FALSE, eval=TRUE ,message=FALSE ,warning=FALSE----
#Remove the file from vignette folder
file.remove("homeobox.png")


## ----summary, eval=FALSE , echo=TRUE-------------------------------------
## library(LowMACA)
## Genes <- c("ADNP","ALX1","ALX4","ARGFX","CDX4","CRX"
## 			,"CUX1","CUX2","DBX2","DLX5","DMBX1","DRGX"
## 			,"DUXA","ESX1","EVX2","HDX","HLX","HNF1A"
## 			,"HOXA1","HOXA2","HOXA3","HOXA5","HOXB1","HOXB3"
## 			,"HOXD3","ISL1","ISX","LHX8")
## Pfam <- "PF00046"
## lm <- newLowMACA(genes=Genes , pfam=Pfam)
## lmParams(lm)$tumor_type <- c("skcm" , "stad" , "ucec" , "luad" , "lusc" , "coadread" , "brca")
## lmParams(lm)$min_mutation_number <- 0
## lm <- setup(lm , mail="lowmaca@gmail.com")
## lm <- entropy(lm)
## lfm(lm)
## bpAll(lm)
## lmPlot(lm)
## protter(lm)


## ----info,echo=TRUE------------------------------------------------------
sessionInfo()