## ----width_control, echo = FALSE------------------------------------------------------------------
options(width = 100)

## ----BiocManager_install, eval = FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE)) {
#      install.packages("BiocManager")
#  }
#  BiocManager::install("Pedixplorer")

## ----library_charge-------------------------------------------------------------------------------
library(Pedixplorer)

## ----Pedigree_creation----------------------------------------------------------------------------
data("sampleped")
print(sampleped[1:10, ])
ped <- Pedigree(sampleped[c(3, 4, 10, 35, 36), ])
print(ped)

## ----ped1-----------------------------------------------------------------------------------------
ped <- Pedigree(sampleped)
print(famid(ped))
ped1 <- ped[famid(ped) == "1"]
summary(ped1)
plot(ped1)

## ----ped1_title-----------------------------------------------------------------------------------
plot(ped1, title = "Pedigree 1", legend = TRUE, leg_loc = c(5, 15, 4.5, 5))

## ----datped2--------------------------------------------------------------------------------------
datped2 <- sampleped[sampleped$famid == 2, ]
datped2[datped2$id %in% 203, "sex"] <- 2
datped2 <- datped2[-which(datped2$id %in% 209), ]

## ----fixped2--------------------------------------------------------------------------------------
tryout <- try({
    ped2 <- Pedigree(datped2)
})
fixped2 <- with(datped2, fix_parents(id, dadid, momid, sex))
fixped2
ped2 <- Pedigree(fixped2)
plot(ped2)

## ----calc_kinship---------------------------------------------------------------------------------
kin2 <- kinship(ped2)
kin2[1:9, 1:9]

## ----kin_all--------------------------------------------------------------------------------------
ped <- Pedigree(sampleped)
kin_all <- kinship(ped)
kin_all[1:9, 1:9]
kin_all[40:43, 40:43]
kin_all[42:46, 42:46]

## ----kin_twins------------------------------------------------------------------------------------
reltwins <- as.data.frame(rbind(c(206, 207, 1, 2), c(125, 126, 1, 1)))
colnames(reltwins) <- c("indId1", "indId2", "code", "family")
ped <- Pedigree(sampleped, reltwins)

kin_all <- kinship(ped)
kin_all[24:27, 24:27]
kin_all[46:50, 46:50]

## ----status---------------------------------------------------------------------------------------
df2 <- sampleped[sampleped$famid == 2, ]
names(df2)
df2$status <- c(1, 1, rep(0, 12))
ped2 <- Pedigree(df2)
summary(status(ped(ped2)))
plot(ped2)

## ----labels---------------------------------------------------------------------------------------
mcols(ped2)$Names <- c(
    "John\nDalton", "Linda", "Jack", "Rachel", "Joe", "Deb",
    "Lucy", "Ken", "Barb", "Mike", "Matt",
    "Mindy", "Mark", "Marie\nCurie"
)
plot(ped2, label = "Names")

## ----two_affection--------------------------------------------------------------------------------
mcols(ped2)$bald <- as.factor(c(0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1))
ped2 <- generate_colors(ped2, col_aff = "bald", add_to_scale = TRUE)
plot(ped2, legend = TRUE)

## ----twins----------------------------------------------------------------------------------------
## create twin relationships
rel_df <- data.frame(
    indId1 = c("210", "212"),
    indId2 = c("211", "213"),
    code = c(1, 3),
    family = c("2", "2")
)
rel(ped2) <- upd_famid_id(with(rel_df, Rel(indId1, indId2, code, family)))
plot(ped2)

## ----inbreeding-----------------------------------------------------------------------------------
indid <- 195:202
dadid <- c(NA, NA, NA, 196, 196, NA, 197, 199)
momid <- c(NA, NA, NA, 195, 195, NA, 198, 200)
sex <- c(2, 1, 1, 2, 1, 2, 1, 2)
ped3 <- data.frame(
    id = indid, dadid = dadid,
    momid = momid, sex = sex
)

ped4df <- rbind.data.frame(df2[-c(1, 2), 2:5], ped3)
ped4 <- Pedigree(ped4df)
plot(ped4)

## ----spouse---------------------------------------------------------------------------------------
## create twin relationships
rel_df2 <- data.frame(
    id1 = "211",
    id2 = "212",
    code = 4,
    famid = "2"
)
new_rel <- c(rel(ped2), with(rel_df2, Rel(id1, id2, code, famid)))
rel(ped2) <- upd_famid_id(new_rel)
plot(ped2)

## ----plotped1-------------------------------------------------------------------------------------
df1 <- sampleped[sampleped$famid == 1, ]
relate1 <- data.frame(
    id1 = 113,
    id2 = 114,
    code = 4,
    famid = 1
)
ped1 <- Pedigree(df1, relate1)
plot(ped1)

## ----ordering-------------------------------------------------------------------------------------
df1reord <- df1[c(35:41, 1:34), ]
ped1reord <- Pedigree(df1reord, relate1)
plot(ped1reord)

## ----scales modif---------------------------------------------------------------------------------
scales(ped1)
fill(ped1)$fill <- c("green", "blue", "purple")
fill(ped1)$density <- c(30, 15, NA)
fill(ped1)$angle <- c(45, 0, NA)
border(ped1)$border <- c("red", "black", "orange")
plot(ped1, legend = TRUE)

## ----ped2df, eval = FALSE-------------------------------------------------------------------------
#  dfped2 <- as.data.frame(ped(ped2))
#  dfped2

## ----subset---------------------------------------------------------------------------------------
ped2_rm210 <- ped2[-10]
rel(ped2_rm210)
rel(ped2)

## ----subset_more----------------------------------------------------------------------------------
ped2_trim210 <- subset(ped2, "2_210", keep = FALSE)
id(ped(ped2_trim210))
rel(ped2_trim210)
ped2_trim_more <- subset(ped2_trim210, c("2_212", "2_214"), keep = FALSE)
id(ped(ped2_trim_more))
rel(ped2_trim_more)

## ----shrink1--------------------------------------------------------------------------------------
set.seed(200)
shrink1_b30 <- shrink(ped1, max_bits = 30)
print(shrink1_b30[c(2:8)])
plot(shrink1_b30$pedObj)

## ----shrink2--------------------------------------------------------------------------------------
set.seed(10)
shrink1_b25 <- shrink(ped1, max_bits = 25)
print(shrink1_b25[c(2:8)])
plot(shrink1_b25$pedObj)

## ----unrelateds-----------------------------------------------------------------------------------
ped2 <- Pedigree(df2)
set.seed(10)
set1 <- unrelated(ped2)
set1
set2 <- unrelated(ped2)
set2

## ----unrelkin-------------------------------------------------------------------------------------
df2
is_avail <- df2$id[df2$avail == 1]
kin2[is_avail, is_avail]

## -------------------------------------------------------------------------------------------------
sessionInfo()