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Debugging R scripts with command line arguments 1…

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.

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showMethods and selectMethod to find the functions and…

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

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Shuffle sequences in DNASequenceSet lapply or sapply return…

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

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A clever use of geom smooth position =…

A clever use of geom_smooth(position = ‘jitter’) for plots looking like hand-written.

test.dframe <- data.frame(x = rnorm(100), y = rnorm(100), z = rnorm(100)
theme_xkcd <- theme(
    panel.background = element_rect(fill="white"),
    axis.ticks = element_line(colour=NA),
    panel.grid = element_line(colour="white"),
    axis.text.y = element_text(colour=NA),
    axis.text.x = element_text(colour="black"),
    )
 

p <- ggplot(data=pleb.clegg, aes(x=Date, y=Pleb))+
geom_smooth(aes(y=Clegg), colour="gold", size=1, position="jitter", fill=NA)+
geom_smooth(colour="white", size=3, position="jitter", fill=NA)+
geom_smooth(colour="dark blue", size=1, position="jitter", fill=NA)+
geom_text(data=pleb.clegg[10, ], family="Humor Sans", aes(x=Date), colour="gold", y=20, label="Searches for clegg")+
geom_text(data=pleb.clegg[22, ], family="Humor Sans", aes(x=Date), colour="dark blue", y=4, label="Searches for pleb")+
geom_line(aes(y=xaxis), position = position_jitter(h = 0.1), colour="black")+
coord_cartesian(ylim=c(-5, 40))+
labs(x="", y="", title="Pleb vs Clegg: Google Keyword Volumes")+
theme_xkcd

handwritten_plot

http://drunks-and-lampposts.com/2012/10/02/clegg-vs-pleb-an-xkcd-esque-chart/

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R 11/07/2013

Posted from Diigo. The rest of my favorite links are here.

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R 11/06/2013

Posted from Diigo. The rest of my favorite links are here.