ggplot dot plot adjust scale

Question

My data looks like

junc                    old         new
X:65961303-65965481(+)  0.025672937 0.004911527
3:90310183-90313113(-)  0.098444488 0.002132802
6:51414210-51415178(-)  3.05E-05    4.37E-06
10:79322700-79323569(+) 0.33095695  0.302002001
4:122972516-122973173(+)    0.939167683 0.932705233
4:53030079-53033983(+)  0.000233548 0.00081976
13:56185646-56189613(-) 4.85E-10    9.43E-09
13:56189703-56197485(-) 4.82E-07    6.96E-09
11:98577839-98579023(-) 0.001854774 0.000894136
10:90615925-90621493(-) 0.000902529 2.84E-05
10:19614164-19624369(-) 4.38E-08    1.26E-06

I would like to plot a dot plot where my x axis is junc and y axis is value and each junc would ideally have two dots (new and old)

What I have tried so far:

library(ggplot2)
library(reshape2)
dat <- read.delim('~/plot.txt', sep = '\t', header = F)
head(dat)
colnames(dat) = c('junc', 'old', 'new')
head(dat)
mdat <- melt(dat)
head(mdat)

 p = ggplot(mdat, aes(x=mdat$junction, fill=mdat$variable)) + geom_dotplot(binpositions="all")
 p

Figure obtained:

How do i adjust the scale and change the plot in such a way that I can visualize difference is old and new value for each junc.

[edit] figure from AK88 suggestion

EDIT:

> head(mdat)
                   junc variable        value
1   X:65961303-65965481(+)       old 2.567294e-02
2   3:90310183-90313113(-)       old 9.844449e-02
3   6:51414210-51415178(-)       old 3.048876e-05
4  10:79322700-79323569(+)       old 3.309569e-01
5 4:122972516-122973173(+)       old 9.391677e-01
6   4:53030079-53033983(+)       old 2.335478e-04
> 
>head(mlt)
junc variable value
1   X:65961303-65965481(+)  variable   old
2   3:90310183-90313113(-)  variable   old
3   6:51414210-51415178(-)  variable   old
4  10:79322700-79323569(+)  variable   old
5 4:122972516-122973173(+)  variable   old
6   4:53030079-53033983(+)  variable   old

AK88 · Accepted Answer · 2017-06-15 06:30:52Z

1

In your melt specify id.vars = "junc":

mdat = melt(dat, id.vars = "junc")

ggplot(data = mdat, aes(x = junc, y = value, color = variable)) +
  geom_point(position = position_dodge(width = 0.2))

edited Jun 15, 2017 at 6:30

answered Jun 15, 2017 at 6:01

AK88

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12 Comments

novicebioinforesearcher Over a year ago

I have added figure in main question base don your suggestion

AK88 Over a year ago

whoa, wait, can you post the head of your new melted data?

novicebioinforesearcher Over a year ago

junc variable value 1   X:65961303-65965481(+)  variable   old 2   3:90310183-90313113(-)  variable   old 3   6:51414210-51415178(-)  variable   old 4  10:79322700-79323569(+)  variable   old 5 4:122972516-122973173(+)  variable   old 6   4:53030079-53033983(+)  variable   old

AK88 Over a year ago

Can you post it into the body of your post? It is difficult to see the columns here.

novicebioinforesearcher Over a year ago

posted head for both the variable

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