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I have data in the following format. Column V1 is the genomic location of interest, and column V4 and V5 are the minor allele frequencies at two different points in time. I would like to make a simple xy scatter plot with a line connecting the allele frequency for each specific location from timepoint 1 to timepoint 2(plotted on y-axis). (Note, I actually have hundreds to thousands of data points).

   V1    V2      V3          V4          V5
1 153 1/113   1/115 0.008849558 0.008695652
2 390 0/176 150/152 0.000000000 0.986842105
3 445 1/149   1/152 0.006711409 0.006578947
4 507 0/154 144/146 0.000000000 0.986301370
5 619 1/103  99/101 0.009708738 0.980198020
6 649 0/138 120/123 0.000000000 0.975609756

I feel like I should be able to accomplish this with ggplot, but I am not sure how to go about doing so, as I don't know how to specify two y-values for each genomic position, nor specify a column as a category. I suspect the data needs to be reshaped somehow. Any help or suggestions are greatly appreciated!

Update:

Thanks to all who gave me suggestions. I don't think I was very clear about wanting the time points to be my x-axis as opposed to the genomic position - my apologies. Hopefully this picture clarifies that!

I have successfully generated the plot I wished to make with the following code:

ggplot(dat) + geom_segment(aes(x="timepoint 1", y=V4, xend="timepoint2", yend=V5))

and this is what the plot looks like with more data points...

allelefreqtrajectories

I haven't changed the axes titles and played with margins yet, but this is the general idea!

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  • As you are rather new on SO, please take some time to read about Stackoverflow and what to ask. As you will find in these two links, you should "show your work", and "Questions asking for code must include attempted solutions, why they didn't work". Thanks for providing a small, dummy data set! Commented Nov 8, 2013 at 22:35
  • These don't really seem to be what most people would call "time series". Commented Nov 8, 2013 at 23:06

3 Answers 3

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If your example data was in DF, then

ggplot(DF) +
  geom_segment(aes(x=V4, y="timepoint 1", xend=V5, yend="timepoint 2"))

enter image description here

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2 Comments

Thank you! I am going to play with this tomorrow and will report back if it does what I am after tomorrow. I've never used geom_segment(), so I'm excited to try this out!
This works great! I flipped the axes around, and have plotted it with all the data points. I have one data set with three timepoints so next I will be playing with geom_path or geom_line it looks like. Thanks for cluing me in on these functions/layers of ggplot.
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It's not completely clear from the question, but I think this is what you're after:

ggplot(d, aes(x=V1, y=V4, ymin=V4, ymax=V5)) 
  + geom_linerange() 
  + xlab('Genomic location') 
  + ylab('Minor allele frequency')

Docs: http://docs.ggplot2.org/current/geom_linerange.html

enter image description here

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Thank you for the suggestion! I am going to look into the geom_linerange() as this may get at what I am after. I actually want the time points to be the x-axis (the genomic location simply serves as a variable to store the allele freq at the two different time points.)
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with(dat, plot(x=V1, y=V5, ylim=c(0,1) ,type='n',
      xaxt="n", ylab="Allele Frequency", xlab="Genomic Location"))
with(dat, axis(1, V1,V1, cex.axis=0.7)   )
with( dat, arrows(x0=V1,x1=V1+10, y0=V4, y1=V5) )

You can clean up the labeling and tweak colors and arrowhead features:

?arrows

enter image description here

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Thank you for the suggestion. I'm actually looking to have the time points as the x-axis (the genomic location is just how I am storing the allele frequencies at different time points). I won't have a chance to play with the code until tomorrow or Tuesday, but I will report back once I do.
You cannot get worked examples if you don't include values for time in your data.

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