Hi Ana,
I should clarify what I wrote in the previous email. You are expecting
an approximately square plot with a line running at about an angle of
45 degrees from lower left to upper right. However, the range of x and
y values that you are plotting are not approximately equal. This means
that lin
Hi Ana,
I'll do my best. In the attached image, I have placed two green disks
at (0,0) and (1,1). These points are on a line with intercept 0 and
slope 1 as are all the other points on that line. When you ask for an
abline with two unnamed arguments, the first is the intercept and the
second is the
Hi Jim,
I have in my code:
abline(0,1,col='red')
can you please tell me how to change my code to have it indeed running
from 0 to 1?
Thanks
Ana
On Fri, Feb 28, 2020 at 3:34 PM Jim Lemon wrote:
>
> Hi Ana,
> Look carefully at that red line. It goes through (0,0) and scoots off
> the plot at (2.
Hi Ana,
Look carefully at that red line. It goes through (0,0) and scoots off
the plot at (2.5,2.5). As you have specified that intercept and slope
in your code, poor abline is doing the best it can. Do not punish it
for doing what you request.
Jim
On Sat, Feb 29, 2020 at 6:10 AM Ana Marija wrot
Hello,
I made the plot in attach with this function:
qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
{
nn = length(p)
xx = -log10((1:nn)/(nn+1))
plot( xx, -sort(log10(p)),
main = MAIN, sub= SUB, cex.sub=1.3,
xlab=expression(Expected~~-log[10](italic(p))),
ylab=expr
Hi Michael,
Thank you so much for that valuable idea!
I will try first to clump or remove SNPs in LD and maybe the situation
would improve.
But this procedure of yours is definitely something that would come
handy in future!
Cheers,
Ana
On Wed, Nov 13, 2019 at 5:47 AM Michael Dewey wrote:
>
> D
Dear Ana
As others have commented this is getting a bit off-topic but here are
some hints.
It is helpful to distinguish two sorts of plot: archival plots and
impact plots. If you want to have an impact plot which gives you a
picture but possibly at the cost of completeness and accuracy then
Typo: "... from 5.5 million..."
Bert
On Tue, Nov 12, 2019 at 3:11 PM Bert Gunter wrote:
> IMO, this thread has now gone totally off the rails and totally off topic
> -- it is clearly *not* about R programming and totally about statistics.
>
> I believe Ana Marija would do better to get local s
IMO, this thread has now gone totally off the rails and totally off topic
-- it is clearly *not* about R programming and totally about statistics.
I believe Ana Marija would do better to get local statistical help or post
on a statistics or genomics list (stats.stackexchange.com is one such)
where
why I selected only those with P<0.003 to put on QQ plot is because
the original data set contains 5556249 points and when I extract only
P<0.001 I am getting 3713 points. Is there is a way to plot the whole
data set, or choose only the representative points?
On Tue, Nov 12, 2019 at 3:42 PM Ana Ma
the smallest p value in my dataset goes to 9.89e-08. How do I make
that known on the new QQ plot with multiplied with 1000 values
On Tue, Nov 12, 2019 at 3:37 PM Ana Marija wrote:
>
> Just do I need to change the axis when I multiply with 1000 and what
> should I put on my axis?
>
> On Tue, Nov 1
Just do I need to change the axis when I multiply with 1000 and what
should I put on my axis?
On Tue, Nov 12, 2019 at 3:07 PM Ana Marija wrote:
>
> Hi Duncan,
>
> yes I choose for QQ plot only P<1e-3 and multiplying everything with
> 1000 works great!
> This should not in my understanding influen
Hi Duncan,
yes I choose for QQ plot only P<1e-3 and multiplying everything with
1000 works great!
This should not in my understanding influence the interpretation of
the plot, it is only changing the scale of axis.
Thank you so much,
Ana
On Tue, Nov 12, 2019 at 2:51 PM Duncan Murdoch wrote:
>
>
On 12/11/2019 2:56 p.m., Jim Lemon wrote:
I thought about this and did a little study of GWAS and the use of
p-values to assess significant associations. As Ana's plot begins at
values of about 0.001, this seems to imply that almost everything in
the genome is associated to some degree. One expec
That refers to "normally" distributed data (see Greg Snow's comment
below the one you cite). P-values are not necessarily normally
distributed as you can see, and they must have a non-zero mean.
Jim
On Wed, Nov 13, 2019 at 7:07 AM Ana Marija wrote:
>
> Hi,
>
> what I know so far that this kind o
As this is O/T I'll keep it offlist.
Inline:
On Tue, Nov 12, 2019 at 12:00 PM Jim Lemon wrote:
> I thought about this and did a little study of GWAS and the use of
> p-values to assess significant associations. As Ana's plot begins at
> values of about 0.001, this seems to imply that almost ev
Hi,
what I know so far that this kind of QQ plot is an indication that
data has non zero mean:
https://stats.stackexchange.com/questions/280634/how-to-interpret-qq-plot-not-on-the-line
but is that an indication that something is wrong with the analysis?
Thanks
Ana
On Tue, Nov 12, 2019 at 2:00 P
Just a small comment. In GWAS studies p values are considerate to bi
significant whwn p < 10-6 or smaller
regards,
Miloš
On Tue, 12 Nov 2019 at 21:00, Jim Lemon wrote:
> I thought about this and did a little study of GWAS and the use of
> p-values to assess significant associations. As Ana's pl
details about my data if it is helpful:
> median(dd$P,na.rm = FALSE)
[1] 0.000444
> mean(dd$P,na.rm = FALSE)
[1] 0.000461
> min(dd$P,na.rm = FALSE)
[1] 9.89e-08
> max(dd$P,na.rm = FALSE)
[1] 0.001
On Tue, Nov 12, 2019 at 2:07 PM Ana Marija wrote:
>
> Hi,
>
> what I know so far that this kind of
I thought about this and did a little study of GWAS and the use of
p-values to assess significant associations. As Ana's plot begins at
values of about 0.001, this seems to imply that almost everything in
the genome is associated to some degree. One expects that most SNPs
will not be associated wit
I agree with Abby. That would defeat the purpose of a QQ plot.
On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle wrote:
> Hi
>
> I'm not familiar with the qqman package, or GWAS studies.
> However, my guess would be that you're *not* supposed to change the
> position of the line.
>
> On Tue, Nov 12, 20
Hi
I'm not familiar with the qqman package, or GWAS studies.
However, my guess would be that you're *not* supposed to change the
position of the line.
On Tue, Nov 12, 2019 at 11:48 AM Ana Marija wrote:
>
> Hi,
>
> I was using this library, qqman
> https://cran.r-project.org/web/packages/qqman/vi
Hi,
I was using this library, qqman
https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html
to create QQ plot, attached. How would I change this default abline to
start from the beginning of my QQ line?
This is my code:
qq(dd$P, main = "Q-Q plot of GWAS p-values")
Thanks
Ana
Hi Ana Marija,
It would help if we had the data, but I suspect that the data that we
don't have is not uniformly distributed:
library(plotrix)
ams_norm<-rnorm(100)
png("ams_norm.png")
qqunif(rescale(ams_norm,c(0,1)))
dev.off()
ams_unif<-runif(100)
png("ams_unif.png")
qqunif(ams_unif)
dev.off()
Ji
] On Behalf Of
> CHIRIBOGA Xavier
> Sent: February-13-15 4:33 PM
> To: r-help@r-project.org
> Subject: [R] qq-Plot function in version 3.1.2.
>
> Hello! SORRY PROBLEMS WITH FUNCTIONS AGAIN...
>
>
>
> I NEED TO RUN A qqPlot ...I TRIED TO INSTALL IT , BUT A WARNIN
> On Feb 13, 2015, at 1:32 PM, CHIRIBOGA Xavier
> wrote:
>
> Hello! SORRY PROBLEMS WITH FUNCTIONS AGAIN...
>
>
>
> I NEED TO RUN A qqPlot ...I TRIED TO INSTALL IT , BUT A WARNING MESSAGE SAID
>
>
>
> qqPlot is not available for version 3.1.2.
What do you want?
Th
Let's see...
You can spell it qqplot.
You can avoid trying to install nonexistent packages with made-up names.
You can learn to use www.rseek.org
You can learn how to undo your caps lock key. ;)
But do try the first one, in the form of
?qqplot
Sarah
On Fri, Feb 13, 2015 at 4:32 PM, CHIRIBOGA Xa
Hello! SORRY PROBLEMS WITH FUNCTIONS AGAIN...
I NEED TO RUN A qqPlot ...I TRIED TO INSTALL IT , BUT A WARNING MESSAGE SAID
qqPlot is not available for version 3.1.2.
qqPlot(residuals(anc0),id.method="identify")
Error: could not find function "qqPlot"
> install.packages("qqPlot")
Instal
Hello, ron,
have you looked at the help page of qqplot and consequently tried, e.g.,
the following?
xy <- qqplot( rt(300, df = 5), rt(300, df = 5),
xlim = c(-10, 10), ylim = c(0, 10))
str( xy)
Hth -- Gerrit
On Tue, 11 Nov 2014, Ron Michael wrote:
Hi,
I am some questions
Hi,
I am some questions on qq-plot offered by R. Let say I have following qq-plot:
qqplot(rt(300, df = 5), rt(300, df = 5))
However I want to get more controls to define the range of x-axis as well as
y-axis. For example I want to define that, x-axis range will be -10 to 10 and
y-axis range wi
Hello,
I have been using the QQ-Plot functions in R for a while now and I noticed
what I believe is a major inconsistency in the way R estimates and plots
the quantiles of a data set. To see this, let x be a vector of data (or
just simulate some data) say 15 points. Then type
qqnorm(x)
By defaul
On 18/02/12 00:15, nandan amar wrote:
Thanks a lot Turner.
Latter I also tried following :
oo<-quantile(original, probs = seq(0, 1, 0.01), type = 8)
pp<-quantile(predicted, probs = seq(0, 1, 0.01), type = 8)
plot(oo,pp)
But plot for above and following (as you suggested) are not same.
What may
Thanks a lot Turner.
Latter I also tried following :
oo<-quantile(original, probs = seq(0, 1, 0.01), type = 8)
pp<-quantile(predicted, probs = seq(0, 1, 0.01), type = 8)
plot(oo,pp)
But plot for above and following (as you suggested) are not same.
What may be the error ?
Thanks.
On Fri, Feb 17,
On 17/02/12 21:32, nandan amar wrote:
Hello,
I am having two data set original and predicted.
I want to dind QQ-plot fot it.
I tried in following manner :
qq(original~predicted)
and error was :
Error in qq.formula(o ~ p) : y must have exactly 2 levels
There is an option "qtype" which dosent m
Hello,
I am having two data set original and predicted.
I want to dind QQ-plot fot it.
I tried in following manner :
>qq(original~predicted)
and error was :
Error in qq.formula(o ~ p) : y must have exactly 2 levels
There is an option "qtype" which dosent make any difference.
What is the correct
I have found this web page useful
http://www.cms.murdoch.edu.au/areas/maths/statsnotes/samplestats/qqplot.html
Your mileage may vary.
Keith J
"Matevz Pavlic" wrote in message
news:ad5ca6183570b54f92aa45ce2619f9b901208...@gi-zrmk.si...
> Hi all,
>
>
>
> I am trying to test wheater the distribu
age-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of Matevž Pavlic
> Sent: Saturday, April 30, 2011 11:28 AM
> To: r-help@r-project.org
> Subject: [R] QQ plot for normality testing
>
> Hi all,
>
>
>
> I am trying to test wh
, 2011 8:04 PM
To: Matevž Pavlič
Cc: r-help@r-project.org
Subject: Re: [R] QQ plot for normality testing
Hi,
qqnorm basically plots your actual sample values against what the values would
be (approximately) if they were from a normal distribution. qqline() adds a
line through the 1st and 3rd
Hi,
qqnorm basically plots your actual sample values against what the
values would be (approximately) if they were from a normal
distribution. qqline() adds a line through the 1st and 3rd quartiles.
So roughly speaking, if your QQ plot forms a straight line
(particularly the one drawn by qqline)
Hi all,
I am trying to test wheater the distribution of my samples is normal with QQ
plot.
I have a values of water content in clays in around few hundred samples. Is the
code :
qqnorm(w) #w being water content
qqline(w)
sufficient?
How do I know when I get the plo
I would like to change the position of the major tick marks in my qq-plot?
Right now the ticks are set at 5.5, 6.0, 6.5 and 7.0.
I would like them to be at 5.4, 5.6, 5.8, 6.0, 6.2, 6.4, 6.8 and 7.0. So I
would have to remove some of the present ticks. So far I can only add ticks
Hi:
Could you please guide me how to do a qq plot for a 3-parameter lognormal
curve. Here is an example from VGAM package to fit lognormal curve. I need to
do a qq plot to check the fit.
Thanks.
lambda = 4
y = lambda + rlnorm(n <- 1000, mean=1.5, sd=exp(-0.8))
fit = vglm(y ~ 1, lognormal3, trace
Madan Sigdel wrote:
Dear users
I have applied following for my works:
library(car)
x<-scan()
1: 0.92545
2: 0.89321
3: 0.9846
4: 2.9
5: 0.85968
6: 5.2
7: 4.66
8: 1.18788
9: 1.07683
10: 1.07683
11: 8.38
12: 7.423
13: 0.972
14: 3.73
15: 1.06474
16: 1.48
17: 0.92876
18: 2.26493
19: 0.85696
20:
hn Fox wrote:
From: John Fox
Subject: RE: [R] QQ plot
To: "'Madan Sigdel'"
Cc: r-help@r-project.org
Date: Friday, October 9, 2009, 6:58 AM
Dear Madan,
Please see the qq.plot() function in the car package.
I hope this helps,
John
> -Original Message-
> Fr
Hi everyone,
I have recently installed the gap library in order to create QQ plots. The
library works well but was wondering if anyone knew how to create the 95%
confidence bands at the top of the QQ plot?
Many thanks.
Sam.
--
View this message in context:
http://www.nabble.com/QQ-Plot-using-
g
> Subject: [R] QQ plot
>
>
> Dear list
>
> I want to plot the QQ plot with some distributions like geometrical ,
> lognormal and truncated normal with confidence bands. does this options
> available.
> Iam new to R. If you have any scripts and examples please
Dear list
I want to plot the QQ plot with some distributions like geometrical , lognormal
and truncated normal with confidence bands. does this options available.
Iam new to R. If you have any scripts and examples please kindly suggest me.
thank you
madan
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