Array construction in R, Perl, and Python
R:
data
Perl:
@data = (1, 2, 3)
@data[2..3]
%hash = ('a' =>; 'b')
$hash{a}
Python:
data = [1, 2, 3, 'a', 'b', 'c'] data[2:3] tuple = (1, 2, 3, 'a', 'b', https://buycbdproducts.com # immutable dict = {'a': 'America', 'c': 'Canada'} dict['a']
Debugging R scripts with command line arguments.
1. Break up the script into two parts: one for reading the arguments, another one for the analysis.
2. Run R with *-args option. It enters the interactive R session.
Example.
R --args -p ../../input/M00724-foxa1.mat -s ../../input/mouse_promoter_seqs_EPD.fasta -c 0.55 -o testing_
3. Source the the file reading https://buycbdproducts.com arguments.
The file can read the arguments with commandArgs() or by using the getopt package.
4. Source the analysis script.
showMethods() and selectMethod() to find the functions and sources of S3 object in R.
http://tolstoy.newcastle.edu.au/R/help/05/09/12506.html
Shuffle sequences in DNASequenceSet.
lapply() or sapply() return list.
endoapply() returns the same data class, DNASequenceSet.
It is way slower, though.
shuffled.seqs <- endoapply(seqs, sample)
For faster shuffling, look at the link.
http://grokbase.com/t/r/bioconductor/133n8bw1f6/bioc-how-to-operate-on-a-dnastringset-object
Turn numeric into categorical data.
AdultUCI[["age"]] <- ordered(cut(AdultUCI[["age"]], c(15,25,45,65,100)), labels = c("Young", "Middle-aged", "Senior", "Old"))
Change the order of discrete axis.
Generate a factor with reversed levels or use a new ggplot2 option.
Examples.
df$X1 = with(df, factor(X1, levels = rev(levels(X1))))
http://stackoverflow.com/questions/7418191/sorting-dotplot-factor-axis-in-ggplot
flevels <- levels(PlantGrowth$group)
- Reverse the order of a discrete-valued axis
- Get the levels of the factor
flevels <- rev(flevels)
- "ctrl" "trt1" "trt2"
- Reverse the order
bp + scale_x_discrete(limits=flevels)
- "trt2" "trt1" "ctrl"
http://www.cookbook-r.com/Graphs/Axes_(ggplot2)/#reversing-the-direction-of-an-axis
Nested Tmux command.
Screen (vim + gnu screen/tmux) is a great tool for vim that split the pane and send vim buffer to
another pane. (Link: http://www.vim.org/scripts/script.php?script_id=2711)
However, when used the plugin in tmux session, the tmux sessions are nested then the command
is not working properly. Then setting a send prefix in .tmuxrc will solve the nested problem.
Command Sequence for Nested Tmux Sessions
Often I’ll run a multiplexer inside another multiplexer and need a command sequence to send things to the inner session. In Screen, this could be accomplished using C-a a
bind-key a send-prefix
From https://mutelight.org/practical-tmux
Slopegraph in R. Slopegraph shows the change of the quantity or rank.
Beautiful slopegraph example. http://www.drewconway.com/zia/
Theory of slopegraph. http://www.edwardtufte.com/bboard/q-and-a-fetch-msg?msg_id=0003nk
An R and ggplot2 code example of slopegraph https://github.com/leondutoit/slopegraph/blob/master/slopegraph.
R Example code.
Generate sample data
a <- data.frame(go = LETTERS[1:10], enrich = runif(10, 0, 10)) b <- data.frame(go = LETTERS[1:10], enrich = runif(10, 0, 10)) a <- cbind(a, status ='before') b <- cbind(b, status = 'after') ab.melt <- rbind(a, b)
Add an offset column for label positioning
ab.melt <- transform(ab.melt, offset = c(rep(2, times = 10), rep(-2, times = 10))) library(ggplot2) ggplot(data = ab.melt, aes(x = status, y = enrich)) + geom_line(aes(group = go, colour = go)) + geom_text(aes(label = go, hjust = offset, colour = factor(go)))
R function matching a function argument against candidate values.
match.arg(arg, choices, several.ok = FALSE)
arg = match.arg(arg)
How to rank data in R.
rank(a)
Then how to rank the data in reverse order?
rand(-a)