Yilun Zhang - 1 year ago 109

R Question

This is the plot I'm having now.

It's generated from this code:

`ggplot(data1, aes(x=POS,y=DIFF,colour=GT)) +`

geom_point() +

facet_grid(~ CHROM,scales="free_x",space="free_x") +

theme(strip.text.x = element_text(size=40),

strip.background = element_rect(color='lightblue',fill='lightblue'),

legend.position="top",

legend.title = element_text(size=40,colour="lightblue"),

legend.text = element_text(size=40),

legend.key.size = unit(2.5, "cm")) +

guides(fill = guide_legend(title.position="top",

title = "Legend:GT='REF'+'ALT'"),

shape = guide_legend(override.aes=list(size=10))) +

scale_y_log10(breaks=trans_breaks("log10", function(x) 10^x, n=10)) +

scale_x_continuous(breaks = pretty_breaks(n=3)) +

geom_line(stat = "hline",

yintercept = "mean",

size = 1)

The last line, geom_line creates the mean line for each panel.

i.e. If panel1('chr01') has x-axis range from 0 to 100,000,000, I would want to have the mean value for each 1,000,000 range.

mean1 = mean(x=0 to x=1,000,000)

mean2 = mean(x=1,000,001 to x=2,000,000)

like that.

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Answer Source

One way to provide a running mean is with `geom_smooth()`

using the `loess`

local regression method. In order to demonstrate my proposed solution, I created a fake genomic dataset using R functions. You can adjust the `span`

parameter of `geom_smooth`

to make the running mean smoother (closer to 1.0) or rougher (closer to 1/number of data points).

```
# Create example data.
set.seed(27182)
y1 = rnorm(10000) +
c(rep(0, 1000), dnorm(seq(-2, 5, length.out=8000)) * 3, rep(0, 1000))
y2 = c(rnorm(2000), rnorm(1000, mean=1.5), rnorm(1000, mean=-1, sd=2),
rnorm(2000, sd=2))
y3 = rnorm(4000)
pos = c(sort(runif(10000, min=0, max=1e8)),
sort(runif(6000, min=0, max=6e7)),
sort(runif(4000, min=0, max=4e7)))
chr = rep(c("chr01", "chr02", "chr03"), c(10000, 6000, 4000))
data1 = data.frame(CHROM=chr, POS=pos, DIFF=c(y1, y2, y3))
# Plot.
p = ggplot(data1, aes(x=POS, y=DIFF)) +
geom_point(alpha=0.1, size=1.5) +
geom_smooth(colour="darkgoldenrod1", size=1.5, method="loess", degree=0,
span=0.1, se=FALSE) +
scale_x_continuous(breaks=seq(1e7, 3e8, 1e7),
labels=paste(seq(10, 300, 10)), expand=c(0, 0)) +
xlab("Position, Megabases") +
theme(axis.text.x=element_text(size=8)) +
facet_grid(. ~ CHROM, scales="free", space="free")
ggsave(filename="plot_1.png", plot=p, width=10, height=5, dpi=150)
```

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