## Getting help
help("mean")  ## or
?mean

# for a particular package
vignette("extending-ggplot2")
vignette("phyloseq-basics")

## Calculator
2+2

## Assigning a value to a variable
a <- 2*4 ## or a = 2*4 (the # sign signals a comment)
a
a/2
a

## Changing the value of a variable
a <- 4
a

b <- a; b <- 8
a; b

## Elementary modes in R
## ----numeric-------------------------------------------------------------
x <- 1
class(x)
## ----character-----------------------------------------------------------
x <- "hello"
class(x)

## ----logical-------------------------------------------------------------
x <- TRUE ## or FALSE
class(x)

## Special values
a <- NA; length(a); is.na(a)

#############
## VECTORS ## 
#############

## ----c-command-----------------------------------------------------------
x <- c(2, 4, 8, 9, 0)
x ## prints x

## ----subsetting-vector-1-------------------------------------------------
x[1] ## first element

## ----subsetting-vector-2-------------------------------------------------
x[c(3, 5)] ## third and fifth elements

## ----coercion-vector-1---------------------------------------------------
c(3.4, 2, TRUE)

## ----coercion-vector-2---------------------------------------------------
c(3.4, "MaIAGE", TRUE)

## ----named-vector--------------------------------------------------------
x <- c("A" = 1, "B" = 4, "C" = 9)
x

## ----named-vector-1------------------------------------------------------
x[1]

## ----named-vector-2------------------------------------------------------
x["C"]

## ----named-vector-3------------------------------------------------------
x <- c(1, 4, 9)
x
names(x) <- c("first", "second", "third")
x

## Try to guess the result
x <- c("O", "G", "F", "S", "R")
x[c(3, 5, 1, 2, 4)]


## ----logical-indexing-1--------------------------------------------------
x <- 1:6
x
index <- c(TRUE, FALSE, TRUE, TRUE, FALSE, FALSE)
x[index] ## = x[c(1, 3, 4)] 

## ----logical-indexing-2--------------------------------------------------
index <- c(TRUE, FALSE, TRUE, TRUE, FALSE, FALSE, TRUE)
x[index] ## = x[c(1, 3, 4, 7)] but x[7] does not exist

## Exercice
rank <- c("Order", "Kingdom", "Genus", "Class", "Family",  "Species", "Phylum")
# Create a new_rank vector based on rank in the correct order
reordered_rank <- rank[c(2, 7, 4, 1, 5, 3, 6)]


############
## MATRIX ## 
############

## ----matrices------------------------------------------------------------
x <- matrix(1:18, nrow = 3, ncol = 6) ## compare to x <- matrix(1:18, nrow = 3, ncol = 6, byrow = TRUE)
x
x[2, 4] ## element in 2nd row, 4th column

## ----indexing-matrix-1---------------------------------------------------
x[, 2] ## 2nd column 

## ----indexing-matrix-2---------------------------------------------------
x[2, ] ## 2nd row 

## Try to guess the result
x <- as.matrix(read.csv("data/introR/matrix.tsv", row.names=1, sep="\t"))
x
x[ , 3]
x["otu_2",]
x[c(1, 2), ]
x[c(1, 3), c(2, 3)]

## How to access to the count of sample2 for otu_3 ?
x["otu_3", "sample2" ]
x["otu_3", 2 ]
x[3, 2 ]
x[3, "sample2" ]

############
## FACTOR ## 
############

## ----factor-example------------------------------------------------------
x <- factor(c("male", "male", "female", "male", "female"))
class(x)

## ----levels--------------------------------------------------------------
levels(x)

## ----relevel-------------------------------------------------------------
x <- as.factor(c("strong", "strong", "weak", "middle", "weak"))
levels(x)
y <- factor(x, c("weak", "middle", "strong"))
levels(y)

################
## DATA FRAME ## 
################

## ----data.frame, echo = -1-----------------------------------------------
x <- data.frame(number = c(1:4), 
                group = factor(c("A", "A", "B", "B")), 
                desc = c("riri", "fifi", "lulu", "picsou"))

## Characteristics of x
x
class(x)
class(x[,1])
class(x[,2])

## ----data.frame-----------------------------------------------
x <- data.frame(number = c(1:4), 
                group = factor(c("A", "A", "B", "B")),
                desc = c("riri", "fifi", "lulu", "picsou"),
                stringsAsFactors = FALSE)

x[2, "desc"] ## or x[2, 3] 


dim(x); nrow(x); ncol(x)
x$group

## Exercice setup
x <- data.frame(ID = 1:10, 
                group = rep(c("A", "B"), each = 5), 
                value = rnorm(10))
x
## Try to guess the result
ii <- 1:5
df <- x[ii, c("ID", "value")]
df
df[ , 2]
class(df[ , 2])
df[2, ]
class(df[2, ])

#############################
## BUILDING LOGICAL FILTER ## 
#############################

x <- 11:15
x
z <- (x < 13); z ## the first command returns a logical vector
z <- (x < 14) & (x > 11); z ## logical AND
z <- (x < 12) | (x > 14); z ## logical OR
!z ## logical not
which(z)
z <- which(x < 14)
x[z]
x[x < 14]

#############
## GGPLOT2 ## 
#############

## ----load-ggplot, cache = FALSE------------------------------------------
library(ggplot2)

## ----diamonds------------------------------------------------------------
data(diamonds) ## import datasets
class(diamonds) 
head(diamonds) ## first line of data.frame
help(diamonds)
## ----ggplot-first-example------------------------------------------------
## set base plot, x coordinate is carat, y is price
p <- ggplot(diamonds, aes(x = carat, y = price))
## Add a layer to represent data as point
p1 <- p + geom_point()
plot(p1)

## ----ggplot-color-example------------------------------------------------
## set base plot, x coordinate is carat, y is price colored by cut
p <- ggplot(diamonds, aes(x = carat, y = price, color=cut))
## Add a layer to represent data as point
p2 <- p + geom_point()
plot(p2)
## OR
p <- ggplot(diamonds, aes(x = carat, y = price))
## Add a layer to represent data as point
p2 <- p + geom_point(aes(color=cut))
plot(p2)

## ----ggplot-boxplot-example------------------------------------------------
## Add a layer to represent data as boxplot
p <- ggplot(diamonds, aes(x = cut, y = price))
p3 <- p + geom_boxplot()
plot(p3)
# colored by clarity
p4 <- ggplot(diamonds, mapping = aes(x = cut, y = price, color=clarity)) + geom_boxplot()
plot(p4)

########## FACETTING
## ----facet_wrap, fig.width = 10, fig.height = 4--------------------------
## facet along cut
p5 <- p2+ facet_wrap(~ cut)
plot(p5)

## ----facet_grid, fig.width = 10, fig.height = 2.5------------------------
## facet along cut, only points from a given cut appear in a facet 
p6 <- p2 + facet_grid(~ cut)
plot(p6)

## ----facet_grid-2-factors, fig.width = 10, fig.height = 5, size = "tiny"----
## facet along clarity (rows) * cut (column)
p7 <- p2 + facet_grid(clarity ~ cut) 
plot(p7)

## On boxplot
p8 <- p4 + facet_wrap(~cut)
plot(p8)

## free x
p9 <- p4 + facet_wrap(~cut, scales="free_x")
plot(p9)

## ----palette-------------------------------------------------------------
palette <- c("black", "red", "blue", "magenta", "gray")
names(palette) <- c("Fair", "Good", "Very Good", "Premium", "Ideal")

## ----second-example-1, size = "tiny", fig.height = 4.5-------------------
## Manual color scale
p6.1 <- p6 + scale_color_manual(values = palette)
plot(p6.1)

## ----second-example-2, size = "tiny", fig.height = 4.5-------------------
## Use built-in color palette
p7.1 <- p7 + scale_color_brewer()
plot(p7.1)

## Add title
p10 <- p9 + ggtitle("Diamond prices as a function of clarity") +
xlab("Diamond clarity") + ylab("Diamond price")
plot(p10)

## Add title (center)
p10 <- p9 + ggtitle("Diamond prices as a function of clarity") +
    xlab("Diamond clarity") + ylab("Diamond price")+ theme(plot.title = element_text(hjust = 0.5))
plot(p10)

################
## GO FURTHER ##
################

#################
## CONVERSIONS ## 
#################

## Examples 
as.integer("5")
as.logical(0.0)
as.numeric(TRUE)
as.character(TRUE)
as.numeric("5.56")
as.logical(2)
as.integer("INRA")

## Try to guess the result: integer
as.integer(2/3)
as.integer(5.67)
as.integer(FALSE)
as.integer(TRUE)
as.integer("5.67")
as.integer("MaIAGE")

## Try to guess the result: numeric
as.numeric(2/3)
as.numeric(5.67)
as.numeric(FALSE)
as.numeric(TRUE)
as.numeric("5.67")
as.numeric("MaIAGE")

## Try to guess the result: character
as.character(2/3)
as.character(5.67)
as.character(FALSE)
as.character(TRUE)
as.character(5)
as.character(5+7)

## Try to guess the result: logical
as.logical(2/3)
as.logical(0)
as.logical("45")
as.logical("MaIAGE")

## Guess the result : 
TRUE + TRUE + FALSE * TRUE + TRUE * TRUE 

## ----converting-vector-1-------------------------------------------------
as.numeric(x) ## 1="a", 2="b"
as.character(x)

## ----converting-vector-2-------------------------------------------------
as.integer(y) ## 1="b", 2="a"
as.character(y)