This is some plain text.
More plain text.
This is an R Markdown document. Markdown is a simple formatting syntax for authoring documents. Text you type here will appear as text in the report that's produced.
Formatting is easy. This is bold text, this is italic text, and this is fixed-width text.
Create blockquotes with the “>” character:
IT WAS the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to Heaven, we were all going direct the other way- in short, the period was so far like the present period, that some of its noisiest authorities insisted on its being received, for good or for evil, in the superlative degree of comparison only.
This is a “chunk” of R code. The code is actually run, and the results are printed to the output.
setwd("/Users/sdt5z/Dropbox/code/projects/intro-r-lifesci/knitr_live_demo/")
chromstats <- read.table("chromstats.txt", header = TRUE)
chromstats
## chr length variations
## 1 1 249250621 4401091
## 2 2 243199373 4607702
## 3 3 198022430 3894345
## 4 4 191154276 3673892
## 5 5 180915260 3436667
## 6 6 171115067 3360890
## 7 7 159138663 3045992
## 8 8 146364022 2890692
## 9 9 141213431 2581827
## 10 10 135534747 2609802
## 11 11 135006516 2607254
## 12 12 133851895 2482194
## 13 13 115169878 1814242
## 14 14 107349540 1712799
## 15 15 102531392 1577346
## 16 16 90354753 1747136
## 17 17 81195210 1491841
## 18 18 78077248 1448602
## 19 19 59128983 1171356
## 20 20 63025520 1206753
## 21 21 48129895 787784
## 22 22 51304566 745778
## 23 23 155270560 2174952
## 24 24 59373566 286812
## 25 25 16569 929
summary(chromstats)
## chr length variations
## Min. : 1 Min. :1.66e+04 Min. : 929
## 1st Qu.: 7 1st Qu.:7.81e+07 1st Qu.:1448602
## Median :13 Median :1.34e+08 Median :2174952
## Mean :13 Mean :1.24e+08 Mean :2230347
## 3rd Qu.:19 3rd Qu.:1.59e+08 3rd Qu.:3045992
## Max. :25 Max. :2.49e+08 Max. :4607702
We're back in plain text world here.
You can also embed plots, for example:
library(ggplot2)
qplot(chr, length, geom = "bar", data = chromstats, stat = "identity", main = "Chromosome lengths")
qplot(length, variations, data = chromstats, main = "Number of SNPs vs. Chromosome Length")
