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Multiple histograms in a plot using ggplot2 ggplot…

Multiple histograms in a plot using ggplot2.

ggplot(test.melt, aes(x = value, fill = sample)) + geom_histogram(alpha = 0.3, position = 'identity', aes(y = ..density..)) + geom_density(alpha = 0.3, position = 'identity')

Be careful. The default value for the

position

parameter is different the histogram and density plot. So set the parameter explicitly.

Identity: overlap the two histograms.
stack: stack the two histograms on top of another.
For more options, check Position adjustments in
http://docs.ggplot2.org/current/index.html

Default parameters of histogram and density.

geom_histogram(mapping = NULL, data = NULL, stat = "bin", position = "stack", ...)
stat_density(mapping = NULL, data = NULL, geom = "area", position = "stack", adjust = 1,
  kernel = "gaussian", trim = FALSE, na.rm = FALSE, ...)
geom_density(mapping = NULL, data = NULL, stat = "density", position = "identity",
  na.rm = FALSE, ...)
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To change two vertically split windows to horizontally…

To change two vertically split windows to horizontally split

Ctrl-W t Ctrl-W K
Horizontally to vertically:

Ctrl-W t Ctrl-W H
Explanations:

Ctrl-W t makes the first (topleft) window current
Ctrl-W K moves the current window to full-width at the very top
Ctrl-W H moves the current window to full-height at far left

http://stackoverflow.com/questions/1269603/to-switch-from-vertical-split-to-horizontal-split-fast-in-vim

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Find duplicate or unique records in unix sort…

Find duplicate or unique records in unix

sort is essential because uniq find successive identical lines.
Unique records

cat data.txt | sort | uniq

Duplicate records

cat data.txt | sort | uniq -d
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Using gff format in IGV 1 Do not…

Using gff format in IGV.

1. Do not omit the first line, especially for GFF 3.
As IGV supports both of GFF ver 2 and GFF ver 3, the file needs to be distinguished.
Do not miss the first line

##gff-version    3

2. Make sure tab is used to separate fields.
Even for the first line, there must be a tab between gff-version and 3.
No space.

Here are the specifications.

GFF version 2
http://www.sanger.ac.uk/resources/software/gff/spec.html

GFF version 3
http://www.sequenceontology.org/gff3.shtml

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Index fasta file generating fai file to use…

Index fasta file – generating fai file – to use with IGV or bedtools.

samtools faidx reference.fasta

http://genomeview.org/content/preparing-fasta-files

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Convert all tabs to spaces and vice versa…

Convert all tabs to spaces and vice versa.

You can use the :retab command to convert all existing tabs to spaces. You can do both in one command:

:set et|retab

You can also convert spaces to tabs:

:set noet|retab!

http://vim.wikia.com/wiki/Super_retab

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Vim plugin surround Normal mode ds delete a…

Vim plugin surround

Normal mode
———–
ds – delete a surrounding
cs – change a surrounding
ys – add a surrounding
yS – add a surrounding and place the surrounded text on a new line + indent it
yss – add a surrounding to the whole line
ySs – add a surrounding to the whole line, place it on a new line + indent it
ySS – same as ySs

Visual mode
———–
s – in visual mode, add a surrounding
S – in visual mode, add a surrounding but place text on new line + indent it

http://www.catonmat.net/blog/vim-plugins-surround-vim/

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http jeromyanglim blogspot ca 2010 05 abbreviations of…

http://jeromyanglim.blogspot.ca/2010/05/abbreviations-of-r-commands-explained.html

250+ R commands.
Often times R users suffer from difficulties finding what commands are available for a specific process.
This lists 250+ R commands in table.