---
layout: post
title: "ggplot2: Data"
published: yes
---

## Gói `plyr`

### Làm việc với dữ liệu

```{r manipulate}
library(plyr)
library(ggplot2)
options(digits = 2, width = 60, max.print = 500)

# Select the smallest diamond in each colour
ddply(diamonds, .(color), subset, carat == min(carat))

# Select the two smallest diamonds
ddply(diamonds, .(color), subset, order(carat) <= 2)

# Select the 1% largest diamonds in each group
ddply(diamonds, .(color), subset, carat > 
  quantile(carat, 0.99))

# Select all diamonds bigger than the group average
ddply(diamonds, .(color), subset, price > mean(price))

# Within each colour, scale price to mean 0 and variance 1
ddply(diamonds, .(color), transform, price = scale(price))

# Subtract off group mean
ddply(diamonds, .(color), transform, 
  price = price - mean(price))

nmissing <- function(x) sum(is.na(x))
nmissing(msleep$name)
nmissing(msleep$brainwt)

nmissing_df <- colwise(nmissing)
nmissing_df(msleep)
# This is shorthand for the previous two steps
colwise(nmissing)(msleep)

msleep2 <- msleep[, -6] # Remove a column to save space
numcolwise(median)(msleep2, na.rm = T)
numcolwise(quantile)(msleep2, na.rm = T)
numcolwise(quantile)(msleep2, probs = c(0.25, 0.75), 
  na.rm = T)

ddply(msleep2, .(vore), numcolwise(median), na.rm = T)
ddply(msleep2, .(vore), numcolwise(mean), na.rm = T)

my_summary <- function(df) {
  with(df, data.frame(
    pc_cor = cor(price, carat, method = "spearman"),
    lpc_cor = cor(log(price), log(carat))
  ))
}
ddply(diamonds, .(cut), my_summary)
ddply(diamonds, .(color), my_summary)
```

### Vẽ biểu đồ

```{r gplot}
library(ggplot2)

# Vẽ đường smooth tự động bằng ggplot2
qplot(carat, price, data = diamonds, geom = "smooth", 
  color = color)
dense <- subset(diamonds, carat < 2)
qplot(carat, price, data = dense, geom = "smooth", 
  colour = color,  fullrange = TRUE)

# Vẽ đường smooth bằng tay
library(mgcv)
smooth <- function(df) {
  mod <- gam(price ~ s(carat, bs = "cs"), data = df)
  grid <- data.frame(carat = seq(0.2, 2, length = 50))
  pred <- predict(mod, grid, se = T)
  
  grid$price <- as.vector(pred$fit)
  grid$se <- as.vector(pred$se.fit)
  grid
}
smoothes <- ddply(dense, .(color), smooth)
qplot(carat, price, data = smoothes, colour = color, 
  geom = "line")
qplot(carat, price, data = smoothes, colour = color, 
  geom = "smooth", ymax = price + 2 * se, ymin = price - 2 * se)

mod <- gam(price ~ s(carat, bs = "cs") + color, data = dense)
grid <- with(diamonds, expand.grid(
  carat = seq(0.2, 2, length = 50),
  color = levels(color)
))
grid$pred <- predict(mod, grid)
qplot(carat, pred, data = grid, colour = color, geom = "line")
```

## Gói `reshape`

### Định dạng rộng

```{r wide}
qplot(date, uempmed, data = economics, geom = "line")
qplot(date, unemploy, data = economics, geom = "line")
qplot(unemploy, uempmed, data = economics) + geom_smooth()
```

### Biểu diễn 2 số liệu khác độ đo

```{r long & wide}
ggplot(economics, aes(date)) + 
  geom_line(aes(y = unemploy, colour = "unemploy")) + 
  geom_line(aes(y = uempmed, colour = "uempmed")) + 
  scale_colour_hue("variable")

library(reshape2)
emp <- melt(economics, id = "date", 
  measure = c("unemploy", "uempmed"))
qplot(date, value, data = emp, geom = "line", colour = variable)
```

Có 2 lựa chọn để xử lý những số liệu không cùng độ đo:

```{r rescale & facet}
# Rescaling
range01 <- function(x) {
  rng <- range(x, na.rm = TRUE)
  (x - rng[1]) / diff(rng)
}
emp2 <- ddply(emp, .(variable), transform, value = range01(value))
qplot(date, value, data = emp2, geom = "line", 
  colour = variable, linetype = variable)

# Faceting
qplot(date, value, data = emp, geom = "line") + 
  facet_grid(variable ~ ., scales = "free_y")
```

### Tọa độ song song

```{r data}
popular <- subset(movies, votes > 1e4)
ratings <- popular[, 7:16]
ratings$.row <- rownames(ratings)
molten <- melt(ratings, id = ".row")
```

```{r plot}
# mặc định
pcp <- ggplot(molten, aes(variable, value, group = .row))
pcp + geom_line()
# thêm `alpha`
pcp + geom_line(colour = alpha("black", 1 / 20))
# thêm `jitter`
jit <- position_jitter(width = 0.25, height = 2.5)
pcp + geom_line(position = jit)
# thêm alpha cho jitter
pcp + geom_line(colour = alpha("black", 1 / 20), position = jit)
```

```{r data2}
cl <- kmeans(ratings[1:10], 6)
ratings$cluster <- reorder(factor(cl$cluster), popular$rating)
levels(ratings$cluster) <- seq_along(levels(ratings$cluster))
molten <- melt(ratings, id = c(".row", "cluster"))
```

```{r plot2}
pcp_cl <- ggplot(molten, 
  aes(variable, value, group = .row, colour = cluster)) 
pcp_cl + geom_line(position = jit, alpha = 1/5)
pcp_cl + stat_summary(aes(group = cluster), fun.y = mean, 
  geom = "line")
```

```{r faceting}
library(scales)
pcp_cl + geom_line(position = jit, colour = alpha("black", 1/5)) +
  facet_wrap(~ cluster)
```

## Phương pháp `ggplot()`

### Mô hình đơn giản

```{r simple mol}
qplot(displ, cty, data = mpg) + geom_smooth(method = "lm")
mpgmod <- lm(cty ~ displ, data = mpg)
head(fortify(mpgmod))
```

### Điều chỉnh mô hình

```{r complexer}
mod <- lm(cty ~ displ, data = mpg)
basic <- ggplot(mod, aes(.fitted, .resid)) +
  geom_hline(yintercept = 0, colour = "grey50", size = 0.5) + 
  geom_point() + 
  geom_smooth(size = 0.5, se = F)
basic
# sử dụng residual chuẩn hóa thay vì residual
basic + aes(y = .stdresid)
# Thêm khoảng cách Cook
basic + aes(size = .cooksd) + scale_size_area("Cook's distance")
```


### Thêm biến vào mô hình

```{r add vars}
full <- basic %+% fortify(mod, mpg)
full + aes(colour = factor(cyl))
full + aes(displ, colour = factor(cyl))
```