## ----eval=TRUE, message=FALSE, warning=FALSE----------------------------------
library(rabhit)

## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Load example sequence data and example germline database
data(samples_db, HVGERM, HDGERM)
# Selecting a single individual
clip_db <- samples_db[samples_db$subject=='I5', ]
# Inferring haplotype using J6 as anchor
haplo_db_J6 <- createFullHaplotype(clip_db, toHap_col=c("v_call","d_call"),
                                hapBy_col="j_call", hapBy="IGHJ6", 
                                toHap_GERM=c(HVGERM, HDGERM))

## ----eval=TRUE, warning=FALSE-------------------------------------------------
head(haplo_db_J6,3)

## ----eval=TRUE, warning=FALSE,fig.width=15,fig.height=10----------------------
# Plotting the haplotype map
plotHaplotype(haplo_db_J6)

## ----eval=TRUE, warning=FALSE, fig.width=12, fig.height=8---------------------
# Inferring haplotype using D2-21 as anchor
haplo_db_D2_21 <- createFullHaplotype(clip_db, toHap_col="v_call",
                        hapBy_col="d_call", hapBy="IGHD2-21", toHap_GERM=HVGERM)

## ----eval=TRUE, warning=FALSE-------------------------------------------------
haplo_db_J6[haplo_db_J6$gene == "IGHD2-21", ]

## ----eval=TRUE, warning=FALSE-------------------------------------------------
# rename the subject
haplo_db_J6$subject <- 'J6'
haplo_db_D2_21$subject <- 'D2-21'

# change the anchor gene columns
# For D2-21*01 and J6*03 we will change the column to Anchor_J03_D01
names(haplo_db_J6)[which(names(haplo_db_J6)=='IGHJ6_03')] <- "AnchorJ03D01"
names(haplo_db_D2_21)[which(names(haplo_db_D2_21)=='IGHD2-21_01')] <- "AnchorJ03D01"

# For D2-21*02 and J6*02 we will change the column to Anchor_J02_D02
names(haplo_db_J6)[which(names(haplo_db_J6)=='IGHJ6_02')] <- "AnchorJ02D02"
names(haplo_db_D2_21)[which(names(haplo_db_D2_21)=='IGHD2-21_02')] <- "AnchorJ02D02"

# subsetting the haplo_db_J6 dataset to include only the V genes
haplo_db_J6 <- haplo_db_J6[grep('IGHV',haplo_db_J6$gene),]

# Combining the datasets row wise
haplo_comb <- rbind(haplo_db_J6,haplo_db_D2_21)

## ----eval=TRUE, warning=FALSE, fig.width=14, fig.height=6---------------------
# Plot the haplotype inferred deprogram
hapDendo(haplo_comb)

## ----cache = T, eval=TRUE, warning=FALSE, fig.width=12, fig.height=12---------
# Removing the individual I5_FR1 with the partial V coverage sequence.
clip_dbs <- samples_db[samples_db$subject!='I5_FR2', ]

# Inferred haplotype summary table
haplo_db <- createFullHaplotype(clip_dbs, toHap_col=c("v_call","d_call"),
                        hapBy_col="j_call", hapBy="IGHJ6", toHap_GERM=c(HVGERM, HDGERM))
# Plot the haplotype inferred heatmap
p.list <- hapHeatmap(haplo_db)

# The function return a list with the plot and the optimal width and height
# we can use both parameters to render the plot to the desired size.
width <- p.list$width
height <- p.list$height


## ----echo = F, cache = T, eval=TRUE, warning=FALSE, fig.width=width, fig.height=height----
# Plotting the heatmap
p.list$p

## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Inferring double chromosome deletions
del_binom_db <- deletionsByBinom(clip_dbs)
head(del_binom_db)

## ----eval=TRUE, warning=FALSE,fig.height=9,fig.width=15-----------------------
# Don't plot IGHJ
del_binom_db <- del_binom_db[grep('IGHJ', del_binom_db$gene, invert = T),]
# Inferred deletion summary table
plotDeletionsByBinom(del_binom_db) 

## ----eval=TRUE, warning=FALSE, cache=TRUE-------------------------------------
# Selecting a single individual with partial V coverage
clip_db <- samples_db[samples_db$subject=='I5_FR2', ]

# Detecting non reliable genes
nonReliable_Vgenes <- nonReliableVGenes(clip_db)

## ----eval=TRUE, warning=FALSE, cache=TRUE-------------------------------------
# Inferred deletion summary table
del_binom_db <- deletionsByBinom(clip_db, chain = "IGH", 
                                 nonReliable_Vgenes = nonReliable_Vgenes)

## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Using the deleted_genes and nonRelaible_Vgenes flags 
# to infer haplotype for a partial V coverage sequence dataset
haplo_db <- createFullHaplotype(clip_db, toHap_col=c("v_call","d_call"),
                        hapBy_col="j_call", hapBy="IGHJ6", 
                        toHap_GERM=c(HVGERM, HDGERM),
                        deleted_genes = del_binom_db, 
                        nonReliable_Vgenes = nonReliable_Vgenes)

## ----eval=TRUE, warning=FALSE-------------------------------------------------
# Generate interactive haplotype plot
p <- plotHaplotype(hap_table = haplo_db, html_output = TRUE)

## ----cache=FALSE, eval=FALSE, warning=FALSE-----------------------------------
# # Saving the plot to html output
# htmlwidgets::saveWidget(p, "haplotype.html", selfcontained = T)

## ----cache=FALSE, eval=F, warning=FALSE, message=F----------------------------
# # Plotting the interactive haplotype inference
# p

## ----eval=TRUE, warning=FALSE,fig.height=12,fig.width=15----------------------
# Detecting non reliable genes
nonReliable_Vgenes <- nonReliableVGenes(samples_db)

# Inferring double chromosome deletion
del_binom_db <- deletionsByBinom(samples_db, nonReliable_Vgenes = nonReliable_Vgenes)

# Inferred haplotype summary table for multiple subjects
haplo_db <- createFullHaplotype(samples_db, toHap_col=c("v_call","d_call"), 
                                hapBy_col="j_call", hapBy="IGHJ6", 
                                toHap_GERM=c(HVGERM, HDGERM), 
                                deleted_genes = del_binom_db, 
                                nonReliable_Vgenes = nonReliable_Vgenes)
# plot deletion heatmap
deletionHeatmap(haplo_db)

## ----eval=TRUE, warning=FALSE, cache=T----------------------------------------
# Inferred deletion summary table
del_db <- deletionsByVpooled(samples_db, nonReliable_Vgenes = nonReliable_Vgenes)
head(del_db)

## ----eval=TRUE, warning=FALSE, cache = T,fig.height=4,fig.width=8-------------
# Plot the deletion heatmap
plotDeletionsByVpooled(del_db)