R_Markdown_Examples

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

You can also embed Python code in R markdown.

• First, using the reticulate library, tell R the PATH to python3, which can be found by typing which python3 at the command line.

library(reticulate)
use_python("/usr/bin/python3")

• Here is an example of a Python code chunk.

from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
dna = Seq('ATGACACTGGTA', generic_dna)
print(dna.translate())

## MTLV

You might like to change the size of your plots.

• Here is an example of an R code chunk with fig.width and fig.height options.

library(ggplot2)
df = data.frame(a=rnorm(10),b=rnorm(10))
print(df)

##             a           b
## 1   0.3965548 -1.77727557
## 2   0.4027295 -1.18046985
## 3  -0.4539906  0.18307760
## 4   0.1893731  0.03407790
## 5  -0.1189992  0.72033038
## 6  -1.3177802 -0.75816061
## 7  -0.3735248  0.05699762
## 8  -0.1507561 -1.80780114
## 9   0.4759136  0.55175557
## 10  0.9052857 -0.70662608

ggplot(df, aes(x=a, y=b)) + geom_point()