Thank you so much it is getting better (see attach) when I do:
ggplot( data = tmp.tidy) +geom_point( aes(y = -log10(value),x =
CHR,color=key) ,position = "jitter", size=0.5 )
is there is a way to have separation between every chromosome shown
better and also every number of chromosome shown on
I tried it,
ggplot( data = tmp.tidy) +geom_point( aes(y = BP,x = CHR,color=key)
,position = "jitter" )
I got the attached
On Thu, Jun 11, 2020 at 4:18 PM wrote:
>
> Try adding
> position = "jitter" to the geom_point(...
>
>
>
> On 11 Jun 2020 21:41, Ana Marija wrote:
>
> Hello,
>
> I tried your
Hello,
I tried your code and this is what I got
I really need two groups side by side shown per chromosome as it is here:
https://imgur.com/a/pj40c
on the image there are 4 groups I do have only two
On Thu, Jun 11, 2020 at 11:52 AM wrote:
>
> On 2020-06-11 15:59, Ana Marija wrote:
> > yes all
On 2020-06-11 15:59, Ana Marija wrote:
yes all in one plot.
So I want key (and therefore color)to be "Pold" and "Pnew" as those I
am comparing per CHR
so I used facet_wrap(~CHR) to create a graph per chromosome (on x-axis)
On the end x-axis would have two strikes of Pold and Pnew (different
yes all in one plot.
So I want key (and therefore color)to be "Pold" and "Pnew" as those I
am comparing per CHR
so I used facet_wrap(~CHR) to create a graph per chromosome (on x-axis)
On the end x-axis would have two strikes of Pold and Pnew (different
colors) per one chromosome, and CHR would go
On 2020-06-11 14:54, Ana Marija wrote:
Hello,
I expected it to look like this:
https://imgur.com/a/pj40c
Ah - so all on the one plot? - so you don't want a facet. It puts two
plots side by side (or 22)
where x-axis would be CHR, there is 22 of them
unique(tmp.tidy$CHR)
[1] 1 2 3 4
Hello,
I expected it to look like this:
https://imgur.com/a/pj40c
where x-axis would be CHR, there is 22 of them
> unique(tmp.tidy$CHR)
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
I also have two phenotypes (keys) which I would like to compare
> unique(tmp.tidy$key)
On Wed, 10 Jun 2020 15:36:11 -0500
Ana Marija wrote:
> Hello,
>
> I have a data frame like this:
>
> > head(tmp1)
> CHR BP PoldPnew
> 1 1 785989 0.9521 0.09278
> 2 1 1130727 0.4750 0.19010
> 3 1 1156131 0.5289 0.48520
> 4 1 1158631 0.2554 0.18140
> 5 1 1211292 0.2954
What did you expect?
I'm assuming two plots (based on the subject) and side by side based on
the code (nrow =1)
But you are getting several graphs (facets) on the row and only expected
2?
What is in CHR? i.e. summary(tmp1$CHR)
I'm assuming its not a factor with 2 elements...?
> Hello,
HI Jim
I run it like this:
Rscript --no-save Manhattan_plot.R
and just in case I added: stringsAsFactors=FALSE
so the script looks like this:
library(qqman)
results_log <- read.table("logistic_results_M3.assoc.logistic.C",
head=TRUE,stringsAsFactors=FALSE)
jpeg("M3.assoc.logistic.jpeg")
Hi Ana,
The problem may be that the JPEG device doesn't handle transparency.
Perhaps PNG?
Jim
On Thu, Jun 11, 2020 at 6:48 AM Ana Marija wrote:
>
> Hello,
>
> I have a data frame like this:
>
> > head(tmp1)
> CHR BP PoldPnew
> 1 1 785989 0.9521 0.09278
> 2 1 1130727 0.4750
?dput
We cannot tell how the columns are being stored in memory from your head()
output.
On June 10, 2020 1:36:11 PM PDT, Ana Marija wrote:
>Hello,
>
>I have a data frame like this:
>
>> head(tmp1)
> CHR BP PoldPnew
>1 1 785989 0.9521 0.09278
>2 1 1130727 0.4750 0.19010
>3 1
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