Skip to content

Instantly share code, notes, and snippets.

Mick Watson mw55309

Block or report user

Report or block mw55309

Hide content and notifications from this user.

Learn more about blocking users

Contact Support about this user’s behavior.

Learn more about reporting abuse

Report abuse
View GitHub Profile
View magpy_thoughts
Download Miniconda
Main env (python 3.5):
- snakemake
- Ete3?
- CheckM
- HMMER
- pplacer
- FastTree
- Prodigal
View cowplot_mimic
## functions
plot.histograms <- function(cname="", flip=FALSE, xlim) {
dse <- density(setosa[, cname])
dve <- density(versicolor[, cname])
dvi <- density(virginica[, cname])
ymax <- max(c(dse$y, dve$y, dvi$y))
View sqrt plot
par(mar=c(2,2,1,1))
plot(sqrt, bty="n", xaxt="n", yaxt="n", xlab="", ylab="")
axis(side=1, at=seq(0,1,by=0.2), las=1, labels=FALSE)
axis(side=2, at=seq(0,1,by=0.2), las=2, labels=FALSE)
axis(side=1, at=seq(0,1,by=0.2), las=1, labels=TRUE, tick=FALSE, line=-0.5, cex.axis=0.8)
axis(side=2, at=seq(0,1,by=0.2), las=2, labels=TRUE, tick=FALSE, line=-0.5, cex.axis=0.8)
axis(side=1, at=0.5, labels="x", tick=FALSE, line=0)
View Shuffle fasta output from Polyester
# Polyester (https://github.com/alyssafrazee/polyester) simulates RNA-Seq reads
# Output is FASTA and sorted by input transcript ID
# Some tools don't like this e.g. Salmon, and want a more random order
# Here is a one-liner for shuffling the reads from sample 1 in output directory test.out
cat test.out/sample_01.fasta | paste - - | shuf | awk '{print $1"\n"$2}' > test.out/sample_01.shuf.fasta
View pore_for_nick
mydir <- "/data2/minion/R7/Ebola/PRJEB10571_ERR1014225/014370/pass/"
meta <- read.meta.info(dir=mydir, path.t="/Analyses/Basecall_2D_000/", path.c="Analyses/Basecall_2D_000/")
yield <- plot.cumulative.yield(meta)
plot.length.histogram(meta)
meta.s <- summarise.by.channel(meta)
View brexit
d <- read.csv("http://www.electoralcommission.org.uk/__data/assets/file/0014/212135/EU-referendum-result-data.csv")
vec <- rep(1, nrow(d))
vec[d$Region=="Scotland"] <- 1
vec[d$Region=="North East"] <- 2
vec[d$Region=="North West"] <- 3
vec[d$Region=="East Midlands"] <- 4
vec[d$Region=="West Midlands"] <- 5
vec[d$Region=="Yorkshire and The Humber"] <- 6
vec[d$Region=="Northern Ireland"] <- 7
View yapyap example
YAPYAP first uniquely mapped primary;second uniquely mapped primary 152876366
YAPYAP first uniquely mapped primary;second uniquely mapped primary soft-clipped 7347030
YAPYAP first uniquely mapped primary soft-clipped;second uniquely mapped primary soft-clipped 3420363
YAPYAP first uniquely mapped primary soft-clipped;second uniquely mapped primary 2772544
YAPYAP first unmapped;second unmapped 579939
YAPYAP first uniquely mapped primary;second unmapped 522762
YAPYAP first uniquely mapped primary;second multi-mapped one primary 228682
YAPYAP first multi-mapped one primary;second uniquely mapped primary soft-clipped 183838
YAPYAP first uniquely mapped primary soft-clipped;second multi-mapped one primary 175894
YAPYAP first multi-mapped one primary;second uniquely mapped primary 148302
View EU Remain
# data from https://twitter.com/LukeTurnerEsq/status/738308821207142400
d <- data.frame(min=c(18,30,40,50,60), max=c(29,39,49,59,85), remain=c(73,64,46,45,35), stringsAsFactors=FALSE)
# calc mid-points
mid <- d$min + ((d$max - d$min) / 2)
# fit model and plot
lmfit <- lm(d$remain~mid)
plot(mid, d$remain, pch=16, xlab="Age", ylab="% who support REMAIN in EURef")
abline(lmfit)
View clear RAM
sync; echo 1 > /proc/sys/vm/drop_caches
@mw55309
mw55309 / excel_my_barplot.R
Created Jan 10, 2016
R code to create Excel-like barplot
View excel_my_barplot.R
x <- data.frame(d=runif(12), g=rep(1:4, each =3))
my.col <- c("deepskyblue3","darkorange2","darkgray","gold")
spacer <- c(1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1)
bw <- 0.8
xmax <- (sum(spacer) * bw) + (nrow(x) * bw)
You can’t perform that action at this time.