R help - Mar 2011 - please help ! label selected data points in huge number of data points potentially as high as 50, 000 !

Dear All 
 
I am reposting because I my problem is real issue and I have been working on
this. I know this might be simple to those who know it ! Anyway I need help
!
 
Let me clear my point. I have huge number of datapoints plotted using either
base plot function or xyplot in lattice (I have preference to use lattice). 
         name xvar            p
1       M1    1  0.107983837
2       M2   11  0.209125624
3       M3   21  0.163959428
4       M4   31  0.132469859
5       M5   41  0.086095130
6       M6   51  0.180822010
7       M7   61  0.246619925
8       M8   71  0.147363687
9       M9   81  0.162663127
........
5000 observations  
 
I need to plot xvar (x variable) and p (y variable) using either plot () or
xyplot(). And I want show (print to graph) datapoint name labels to those
rows that have p value < 0.01 (means that they are significant). With my
limited R knowlege I can use text (x,y, labels) option to manually add the
text, but I have huge number of data point(though I provide just 1000 here,
potentially it can go upto 50,000). So I want to display name corresponding
to those observations (rows) that have pvalue less than 0.05 (threshold). 
 
Here is my example dataset and my status:
name <- c(paste ("M", 1:5000, sep = ""))
xvar <- seq(1, 50000, 10)
set.seed(134)
p <- rnorm(5000, 0.15,0.05)
dataf <- data.frame(name,xvar, p)
 
# using lattice (my first preference)
require(lattice) 
xyplot(p ~ xvar, dataf)
 
#I want to display names for the following observation that meet requirement
of p <0.01. 
which (dataf$p < 0.01) 
[1]  811  854 1636 1704 2148 2161 2244 3205 3268 4177 4564 4614 4639 4706
 
Thus significant observations are:
        name  xvar             p
811   M811  8101  0.0050637068
854   M854  8531 -0.0433901783
1636 M1636 16351 -0.0279014039
1704 M1704 17031  0.0029878335
2148 M2148 21471  0.0048898232
2161 M2161 21601 -0.0354130557
2244 M2244 22431  0.0003255200
3205 M3205 32041  0.0079758430
3268 M3268 32671  0.0012797145
4177 M4177 41761  0.0015487439
4564 M4564 45631  0.0024867152
4614 M4614 46131  0.0078381964
4639 M4639 46381 -0.0063151605
4706 M4706 47051  0.0032200517

I want the datapoint (8101, 0.0050637068) with M811 in the plot. Similarly
for all of the above (that are significant). I do not want to label all out
of 5000 who do have p value < 0.01. I know I can add manually - text (8101,
0.0050637068, M811) in plot() in base. 
 
plot (dataf$xvar,p)
text (8101, 0.0050637068, "M811")
text (8531, -0.0433901783, "M854")
 
I need more automation to deal with observations as high as 50,000. In real
sense I do not know how many variables there will be. 
 
You help is highly appreciated. Thank you;
 
Best Regards
 
Umesh R 
 
 
 

  _____  

From: Umesh Rosyara [mailto:rosyaraur@gmail.com] 
Sent: Saturday, March 05, 2011 12:30 PM
To: 'r-help@r-project.org'
Subject: displaying label meeting condition (i.e. significant, i..e p value
less than 005) in plot function 


Dear R users,
 
Here is my problem:
 
# example data
name <- c(paste ("M", 1:1000, sep = ""))
xvar <- seq(1, 10000, 10)
set.seed(134)
p <- rnorm(1000, 0.15,0.05)
dataf <- data.frame(name,xvar, p)
plot (dataf$xvar,p)
abline(h=0.05)
 
# I can know which observation number is less than 0.05 
which (dataf$p < 0.05) 
[1]  12  20  80 269 272 338 366 368 397 403 432 453 494 543 592 691 723 789
811
[20] 854 891 931 955
 
I want to display (label) corresponding names on the plot above: 
means that 12th observation M12, 20th observation M20 and so on. Please note
that I have names not in numerical sequience (rather different names), just
provided for this example to create dataset easily.
 
Thanks in advance
 
Umesh R
 

	[[alternative HTML version deleted]]

I think you've made your problem too complicated.

Given your example below (and THANK YOU for including a workable
example), is this not what you need?

sigdata <- dataf[dataf$p < 0.01,]
plot(dataf$xvar, dataf$p)
text(sigdata$xvar, sigdata$p, sigdata$name)

text() will take vectors of arguments.

Sarah

On Sat, Mar 5, 2011 at 6:29 PM, Umesh Rosyara <rosyaraur at gmail.com>
wrote:
> Dear All
>
> I am reposting because I my problem is real issue and I have been working
on
> this. I know this might be simple to those who know it ! Anyway I need help
> !
>
> Let me clear my point. I have huge number of datapoints plotted using
either
> base plot function or xyplot in lattice (I have preference to use lattice).
> ? ? ? ? name xvar ? ? ? ? ? ?p
> 1 ? ? ? M1 ? ?1 ?0.107983837
> 2 ? ? ? M2 ? 11 ?0.209125624
> 3 ? ? ? M3 ? 21 ?0.163959428
> 4 ? ? ? M4 ? 31 ?0.132469859
> 5 ? ? ? M5 ? 41 ?0.086095130
> 6 ? ? ? M6 ? 51 ?0.180822010
> 7 ? ? ? M7 ? 61 ?0.246619925
> 8 ? ? ? M8 ? 71 ?0.147363687
> 9 ? ? ? M9 ? 81 ?0.162663127
> ........
> 5000 observations
>
> I need to plot xvar (x variable) and p (y variable) using either plot () or
> xyplot(). And I want show (print to graph) datapoint name labels to those
> rows that have p value < 0.01 (means that they are significant). With my
> limited R knowlege I can use text (x,y, labels) option to manually add the
> text, but I have huge number of data point(though I provide just 1000 here,
> potentially it can go upto 50,000). So I want to display name corresponding
> to those observations (rows) that have pvalue less than 0.05 (threshold).
>
> Here is my example dataset and my status:
> name <- c(paste ("M", 1:5000, sep = ""))
> xvar <- seq(1, 50000, 10)
> set.seed(134)
> p <- rnorm(5000, 0.15,0.05)
> dataf <- data.frame(name,xvar, p)
>
> # using lattice (my first preference)
> require(lattice)
> xyplot(p ~ xvar, dataf)
>
> #I want to display names for the following observation that meet
requirement
> of p <0.01.
> which (dataf$p < 0.01)
> [1] ?811 ?854 1636 1704 2148 2161 2244 3205 3268 4177 4564 4614 4639 4706
>
> Thus significant observations are:
> ? ? ? ?name ?xvar ? ? ? ? ? ? p
> 811 ? M811 ?8101 ?0.0050637068
> 854 ? M854 ?8531 -0.0433901783
> 1636 M1636 16351 -0.0279014039
> 1704 M1704 17031 ?0.0029878335
> 2148 M2148 21471 ?0.0048898232
> 2161 M2161 21601 -0.0354130557
> 2244 M2244 22431 ?0.0003255200
> 3205 M3205 32041 ?0.0079758430
> 3268 M3268 32671 ?0.0012797145
> 4177 M4177 41761 ?0.0015487439
> 4564 M4564 45631 ?0.0024867152
> 4614 M4614 46131 ?0.0078381964
> 4639 M4639 46381 -0.0063151605
> 4706 M4706 47051 ?0.0032200517
>
> I want the datapoint (8101, 0.0050637068) with M811 in the plot. Similarly
> for all of the above (that are significant). I do not want to label all out
> of 5000 who do have p value < 0.01. I know I can add manually - text
(8101,
> 0.0050637068, M811) in plot() in base.
>
> plot (dataf$xvar,p)
> text (8101, 0.0050637068, "M811")
> text (8531, -0.0433901783, "M854")
>
> I need more automation to deal with observations as high as 50,000. In real
> sense I do not know how many variables there will be.
>
> You help is highly appreciated. Thank you;
>
> Best Regards
>
> Umesh R
>
>
>
>
-- 
Sarah Goslee
http://www.functionaldiversity.org

Em 5/3/2011 21:29, Umesh Rosyara escreveu:
> Dear All
>
> I am reposting because I my problem is real issue and I have been working
on
> this. I know this might be simple to those who know it ! Anyway I need help
> !
>
> Let me clear my point. I have huge number of datapoints plotted using
either
> base plot function or xyplot in lattice (I have preference to use lattice).
>           name xvar            p
> 1       M1    1  0.107983837
> 2       M2   11  0.209125624
> 3       M3   21  0.163959428
> 4       M4   31  0.132469859
> 5       M5   41  0.086095130
> 6       M6   51  0.180822010
> 7       M7   61  0.246619925
> 8       M8   71  0.147363687
> 9       M9   81  0.162663127
> ........
> 5000 observations
>
> I need to plot xvar (x variable) and p (y variable) using either plot () or
> xyplot(). And I want show (print to graph) datapoint name labels to those
> rows that have p value<  0.01 (means that they are significant). With my
> limited R knowlege I can use text (x,y, labels) option to manually add the
> text, but I have huge number of data point(though I provide just 1000 here,
> potentially it can go upto 50,000). So I want to display name corresponding
> to those observations (rows) that have pvalue less than 0.05 (threshold).
> [snipped]
Umesh,

Given you have been already instructed how to do more or less what you 
intend to, I want to suggest something more simple which given the 
description of your problem seems to me more appropriate:

Create a vector for changing the symbol used to plot the points in the 
scatter diagram:

p.point <- ifelse(p < 0.01,1,19) # for deciding which symbols you want # 
look at example(pch)
plot(xvar, p, , pch=p.points)

HTH

--
Cesar Rabak