test.Rmd

---
title: "R for bioinformatics, data summarisation and statistics"
subtitle: "HUST Bioinformatics course series"
author: "Wei-Hua Chen (CC BY-NC 4.0)"
institute: "HUST, China"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: 
  beamer_presentation:
    theme: AnnArbor
    colortheme: beaver
    fonttheme: structurebold
    highlight: tango
    slide_level: 2
    toc: true
    includes:
      in_header: mystyle.sty
---

```{r include=FALSE}
color_block = function(color) {
  function(x, options) sprintf('\\color{%s}\\begin{verbatim}%s\\end{verbatim}',
                               color, x)
}

## 将错误信息用红色字体显示
knitr::knit_hooks$set(error = color_block('red'))

```

# section 1: TOC

## 前情提要

## 本次提要


# section 2: XX

## some page with layout 

Column 1
--------------------------------------------------

### Chart A

```{r}
```

Column 2
--------------------------------------------------

### Chart B

```{r}
```

### Chart C

```{r}
```

# section 3: XX


# section 5: 小结及作业！

## 本次小结

### XXX

### 相关包

## 公式中的写法之**代数符号**

\FontSmall

|分类| R的表达式                | 显示结果                 |
|---------------------|-------------------------|----|
|代数符号|  ```expression(x + y)```  |  $x + y$         |
||```expression(x - y)```| $x-y$ |
||```expression(x * y)```|$xy$|
||```expression(x / y)```| $x/y$ |
||```expression(x %+-% y)```| $x \pm y$ |
||```expression(x %/% y)```| $x \div y$ |
||```expression(x %*% y)```| $x \times y$ |
||```expression(x %.% y)```|$x \cdot y$|
|| ```expression(x[i])``` | $x_{i}$ |
|| ```expression(x^2)``` | $x^{2}$ |
||```expression(sqrt(x))```| $\sqrt{x}$ |
||```expression(sqrt(x,y))```| $\sqrt[y]{x}$ |
||```expression(list(x,yz))```| $x,y,z$ |


## 希腊字符

代码

\FontSmall 

```{r}
library(ggplot2);
greeks <- c("Alpha", "Beta", "Gamma", "Delta", "Epsilon", "Zeta",
            "Eta", "Theta", "Iota", "Kappa", "Lambda", "Mu",
            "Nu", "Xi", "Omicron", "Pi", "Rho", "Sigma",
            "Tau", "Upsilon", "Phi", "Chi", "Psi", "Omega");

dat <- data.frame( x = rep( 1:6, 4 ), y = rep( 4:1, each = 6), greek = greeks );

plot2 <- 
  ggplot( dat, aes(x=x,y=y) ) + geom_point(size = 0) +
    # 画希腊字符，注意下面两行代码的区别
    geom_text( aes( x, y + 0.1, label = tolower( greek ) ), size = 10, parse = T ) +
    geom_text( aes( x, y - 0.1, label = tolower( greek ) ), size = 5  );
```

## 希腊字符, cont. 

```{r echo=FALSE, message=FALSE, error=FALSE, fig.height=4, fig.width=10}
plot2;
```

## 公式示例

**注** 写公式的方式很多

\FontSmall

```{r fig.width=10, fig.height=4}
eq <- expression(paste(frac(1, sigma*sqrt(2*pi)), " ",
                       plain(e)^{frac(-(x-mu)^2, 2*sigma^2)}));

ggplot( data.frame(x=1:10, y=1:10), aes( x,y ) ) + 
    geom_point( size = 0 ) +
    geom_text(data = NULL, x = 5, y = 5, size = 12,
              label = as.character(eq), parse = TRUE );
```


## 公式示例2 

另一种代入变量值的方法：

\FontSmall

```{r fig.width=10, fig.height=4}
library(ggplot2);
x <- 1.24;
y <- 0.6;

ex <- bquote(.(parse(text=paste( "observed (", "italic(R)^2==", 
                               x,  "^bold(", x, "), n == ", y, ")", 
                               sep = "  " ))) );

ggplot( data.frame(x=1:10, y=1:10), aes( x,y ) ) + geom_point( size = 0 ) +
    geom_text(data = NULL, x = 5, y = 5, size = 8,
              label = as.character(ex), parse = TRUE );
```

## 公式示例3

使用 paste 和 substitute :

\FontSmall

```{r fig.height=4, fig.width=10}
x_mean <- 1.5;
x_sd <- 1.2;

# 表达式
ex <- substitute(
    paste(X[i], " ~ N(", mu, "=", m, ", ", sigma^2, "=", s2, ")"),
    list(m = x_mean, s2 = x_sd^2)
);

# histogram
ggplot( data.frame( x = rnorm(100, x_mean, x_sd) ), aes( x ) ) +
    geom_histogram( binwidth=0.5 ) +
    ggtitle(ex); ## 为什么不需要 parse = TURE ???? 
```


## 下次预告


## 作业

-   ```Exercises and homework``` 目录下 ```talkxx-homework.Rmd``` 文件；

- 完成时间：见钉群的要求

### important
* all codes are available at Github: https://github.com/evolgeniusteam/R-for-bioinformatics