Re: [R] Help me please: gplot, facets_wrap and ordering of x axis dates
Thank you very much for your help and time.
That works very nicelyThanks again!
- Original Message -
From: John Kane
To: David Lyon ; r-help
Cc:
Sent: Wednesday, May 15, 2013 9:36 AM
Subject: Re: [R] Help me please: gplot, facets_wrap and ordering of x axis
dates
My appologies, I was in a rush yesterday and a) completely misread the post
and b) did not scroll down far enough. David W is correct that you need to do
something with the data set. <.6 is not a number.
Also, as David says, it sounds like your coversion using as.Date did not work
out. The difficulty from here is that if is graphs then it sounds like your
actual data.frame is not exactly the same as what I get if I try to read in the
data you included. hat is why supplying the data using something like dput() is
important.
I don't see how got something to plot. However if I get rid of the < in the
text file and read in the data , etc I get something that may look like what
you want. See code below. I renamed the data.frame to dat1, just because it
was handy and renamed the variable date to date1 since date is a reserved word
in R . Type date() to see what I mean.
Again my applogies for completely misreading the problem
John Kane
Kingston ON Canada
#
library(lubridate)
library(ggplot2)
dat1 <- structure(list(id = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 4L,
4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L,
6L, 6L, 6L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 10L,
10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L,
12L, 12L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 17L, 17L, 18L, 18L, 18L,
18L, 18L), date1 = c("8/16/10", "10/25/10", "11/8/10", "11/22/10",
"12/6/10", "8/18/10", "10/25/10", "11/8/10", "11/22/10", "8/20/10",
"10/25/10", "11/8/10", "11/22/10", "12/6/10", "10/26/11", "6/4/09",
"6/18/10", "8/25/10", "9/15/10", "10/25/10", "11/8/10", "11/22/10",
"12/6/10", "11/4/11", "9/23/10", "10/25/10", "11/8/10", "11/22/10",
"12/6/10", "8/25/10", "10/25/10", "11/8/10", "12/6/10", "6/11/12",
"10/6/10", "11/22/10", "2/2/11", "2/16/11", "3/2/11", "3/16/11",
"9/14/10", "2/2/11", "2/16/11", "3/2/11", "3/16/11", "8/20/10",
"2/2/11", "2/16/11", "3/2/11", "3/16/11", "10/26/11", "12/14/10",
"2/2/11", "2/16/11", "3/2/11", "3/16/11", "11/13/09", "8/19/10",
"2/2/11", "2/6/13", "4/24/13", "8/18/10", "10/5/10", "10/27/10",
"2/2/11", "2/16/11", "3/2/11", "3/16/11", "6/29/11", "8/15/11",
"8/15/12", "10/31/12", "12/10/10", "2/2/11", "3/2/11", "3/16/11",
"12/17/10", "1/25/11", "2/2/11", "2/2/11", "2/16/11", "3/2/11",
"3/16/11", "3/20/12", "3/26/12", "3/30/12", "4/2/12", "4/23/12",
"11/17/11", "12/9/11", "2/25/13", "3/11/13", "3/25/13", "4/10/13",
"4/22/13"), value = c(0.16, 0.16, 0.42, 0.81, 0.16, 2.93, 2.4,
1.36, 1.22, 0.77, 0.85, 1.22, 0.21, 1.81, 0.54, 1.33, 1.32, 2.5,
1.3, 1.1, 0.66, 0.84, 7.42, 1.21, 0.97, 2.25, 0.51, 0.53, 0.41,
3.14, 3.58, 2.41, 2.08, 3.2, 0.24, 0.34, 0.58, 0.54, 0.25, 0.39,
0.28, 0.19, 0.42, 0.39, 0.26, 0.16, 0.16, 0.16, 0.16, 1.76, 0.16,
0.48, 1.2, 0.44, 0.32, 0.34, 0.73, 3.32, 13.7, 1.35, 0.85, 0.66,
0.68, 0.53, 0.54, 0.49, 0.31, 0.4, 0.53, 0.55, 0.94, 0.74, 0.4,
0.44, 0.38, 0.43, 0.18, 0.16, 0.53, 0.54, 0.46, 0.29, 0.2, 0.18,
0.23, 0.52, 0.33, 0.3, 3.35, 2.56, 18.1, 14.9, 11.1, 8.47, 15.9
)), .Names = c("id", "date1", "value"), class = "data.frame", row.names = c(NA,
-95L))
str(dat1)
dat1$date1 <- mdy(dat1$date1) # using lubridate
str(dat1) # POSIXct object not date object as in your original code
ggplot(data=dat1) + geom_line(aes(x=date1, y=value, group=id, colour=
factor(id))) + facet_wrap(~id, scales = "free")
#
> -Original Message-
> From: david_ly...@yahoo.com
> Sent: Wed, 15 May
Re: [R] Help me please: gplot, facets_wrap and ordering of x axis dates
Thanks John for your reply.
I did include the data if you scroll down to the end of my original email.
Can someone help me on this?
Thanks
- Original Message -
From: John Kane
To: David Lyon ; r-help
Cc:
Sent: Tuesday, May 14, 2013 4:11 PM
Subject: RE: [R] Help me please: gplot, facets_wrap and ordering of x axis
dates
Thank you for supplying the code. It would be easier to help you if we also
had some data to work with. ?dput
https://github.com/hadley/devtools/wiki/Reproducibility
I think reorder() is likely to do the trick but I don't have enough time to
mock up some data and check at the moment.
Have a look at
http://stackoverflow.com/questions/3744178/ggplot2-sorting-a-plot
Good luck.
John Kane
Kingston ON Canada
> -Original Message-
> From: david_ly...@yahoo.com
> Sent: Tue, 14 May 2013 12:59:07 -0700 (PDT)
> To: r-help@r-project.org
> Subject: [R] Help me please: gplot, facets_wrap and ordering of x axis
> dates
>
> I have a text file of data as below and doing a ggplot line plot of all
> the ids as separate mini line plots which works with the following code.
>
> Problem how do I order the dates for each id plot on the x axis so that
> the dates are going from oldest to most recent
>
>
> Thanks in advance
>
> Dave
>
>
>
>
>
> CODE:
>
> a<-read.table("DATA",header=TRUE);
> b<-a[order(as.Date(a$date, format="%m/%d/%Y")),]
>
> ggplot(data=b) + geom_line(aes(x=date, y=value, group=id, colour=
> factor(id))) + facet_wrap(~id, scales = "free")
>
>
>
>
>
>
> DATA:
>
>
> id date value
> 001 8/16/10 <0.16
> 001 10/25/10 <0.16
> 001 11/8/10 0.42
> 001 11/22/10 0.81
> 001 12/6/10 <0.16
> 002 8/18/10 2.93
> 002 10/25/10 2.4
> 002 11/8/10 1.36
> 002 11/22/10 1.22
> 004 8/20/10 0.77
> 004 10/25/10 0.85
> 004 11/8/10 1.22
> 004 11/22/10 0.21
> 004 12/6/10 1.81
> 004 10/26/11 0.54
> 005 6/4/09 1.33
> 005 6/18/10 1.32
> 005 8/25/10 2.5
> 005 9/15/10 1.3
> 005 10/25/10 1.1
> 005 11/8/10 0.66
> 005 11/22/10 0.84
> 005 12/6/10 7.42
> 005 11/4/11 1.21
> 006 9/23/10 0.97
> 006 10/25/10 2.25
> 006 11/8/10 0.51
> 006 11/22/10 0.53
> 006 12/6/10 0.41
> 008 8/25/10 3.14
> 008 10/25/10 3.58
> 008 11/8/10 2.41
> 008 12/6/10 2.08
> 008 6/11/12 3.2
> 009 10/6/10 0.24
> 009 11/22/10 0.34
> 009 2/2/11 0.58
> 009 2/16/11 0.54
> 009 3/2/11 0.25
> 009 3/16/11 0.39
> 010 9/14/10 0.28
> 010 2/2/11 0.19
> 010 2/16/11 0.42
> 010 3/2/11 0.39
> 010 3/16/11 0.26
> 011 8/20/10 <0.16
> 011 2/2/11 <0.16
> 011 2/16/11 <0.16
> 011 3/2/11 <0.16
> 011 3/16/11 1.76
> 011 10/26/11 <0.16
> 012 12/14/10 0.48
> 012 2/2/11 1.2
> 012 2/16/11 0.44
> 012 3/2/11 0.32
> 012 3/16/11 0.34
> 013 11/13/09 0.73
> 013 8/19/10 3.32
> 013 2/2/11 13.7
> 014 2/6/13 1.35
> 014 4/24/13 0.85
> 014 8/18/10 0.66
> 014 10/5/10 0.68
> 014 10/27/10 0.53
> 014 2/2/11 0.54
> 014 2/16/11 0.49
> 014 3/2/11 0.31
> 014 3/16/11 0.4
> 014 6/29/11 0.53
> 014 8/15/11 0.55
> 014 8/15/12 0.94
> 014 10/31/12 0.74
> 015 12/10/10 0.4
> 015 2/2/11 0.44
> 015 3/2/11 0.38
> 015 3/16/11 0.43
> 016 12/17/10 0.18
> 016 1/25/11 <0.16
> 016 2/2/11 0.53
> 016 2/2/11 0.54
> 016 2/16/11 0.46
> 016 3/2/11 0.29
> 016 3/16/11 0.2
> 016 3/20/12 0.18
> 016 3/26/12 0.23
> 016 3/30/12 0.52
> 016 4/2/12 0.33
> 016 4/23/12 0.3
> 017 11/17/11 3.35
> 017 12/9/11 2.56
> 018 2/25/13 18.1
> 018 3/11/13 14.9
> 018 3/25/13 11.1
> 018 4/10/13 8.47
> 018 4/22/13 15.9
>
>
> __
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[R] Help me please: gplot, facets_wrap and ordering of x axis dates
I have a text file of data as below and doing a ggplot line plot of all the ids
as separate mini line plots which works with the following code.
Problem how do I order the dates for each id plot on the x axis so that the
dates are going from oldest to most recent
Thanks in advance
Dave
CODE:
a<-read.table("DATA",header=TRUE);
b<-a[order(as.Date(a$date, format="%m/%d/%Y")),]
ggplot(data=b) + geom_line(aes(x=date, y=value, group=id, colour= factor(id)))
+ facet_wrap(~id, scales = "free")
DATA:
id date value
001 8/16/10 <0.16
001 10/25/10 <0.16
001 11/8/10 0.42
001 11/22/10 0.81
001 12/6/10 <0.16
002 8/18/10 2.93
002 10/25/10 2.4
002 11/8/10 1.36
002 11/22/10 1.22
004 8/20/10 0.77
004 10/25/10 0.85
004 11/8/10 1.22
004 11/22/10 0.21
004 12/6/10 1.81
004 10/26/11 0.54
005 6/4/09 1.33
005 6/18/10 1.32
005 8/25/10 2.5
005 9/15/10 1.3
005 10/25/10 1.1
005 11/8/10 0.66
005 11/22/10 0.84
005 12/6/10 7.42
005 11/4/11 1.21
006 9/23/10 0.97
006 10/25/10 2.25
006 11/8/10 0.51
006 11/22/10 0.53
006 12/6/10 0.41
008 8/25/10 3.14
008 10/25/10 3.58
008 11/8/10 2.41
008 12/6/10 2.08
008 6/11/12 3.2
009 10/6/10 0.24
009 11/22/10 0.34
009 2/2/11 0.58
009 2/16/11 0.54
009 3/2/11 0.25
009 3/16/11 0.39
010 9/14/10 0.28
010 2/2/11 0.19
010 2/16/11 0.42
010 3/2/11 0.39
010 3/16/11 0.26
011 8/20/10 <0.16
011 2/2/11 <0.16
011 2/16/11 <0.16
011 3/2/11 <0.16
011 3/16/11 1.76
011 10/26/11 <0.16
012 12/14/10 0.48
012 2/2/11 1.2
012 2/16/11 0.44
012 3/2/11 0.32
012 3/16/11 0.34
013 11/13/09 0.73
013 8/19/10 3.32
013 2/2/11 13.7
014 2/6/13 1.35
014 4/24/13 0.85
014 8/18/10 0.66
014 10/5/10 0.68
014 10/27/10 0.53
014 2/2/11 0.54
014 2/16/11 0.49
014 3/2/11 0.31
014 3/16/11 0.4
014 6/29/11 0.53
014 8/15/11 0.55
014 8/15/12 0.94
014 10/31/12 0.74
015 12/10/10 0.4
015 2/2/11 0.44
015 3/2/11 0.38
015 3/16/11 0.43
016 12/17/10 0.18
016 1/25/11 <0.16
016 2/2/11 0.53
016 2/2/11 0.54
016 2/16/11 0.46
016 3/2/11 0.29
016 3/16/11 0.2
016 3/20/12 0.18
016 3/26/12 0.23
016 3/30/12 0.52
016 4/2/12 0.33
016 4/23/12 0.3
017 11/17/11 3.35
017 12/9/11 2.56
018 2/25/13 18.1
018 3/11/13 14.9
018 3/25/13 11.1
018 4/10/13 8.47
018 4/22/13 15.9
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[R] Please Help FDR BH correction of pvalues
I have a matrix of p values below. Column1 are the analytes and the other
columns are p values comparing time points.
How do I convert this table of pvalues into adjust p values for FDR/BH
This is wrong does anyone know how to fix this code
a<-read.table("file", header=T, sep"\t")
b<-as.numeric(as.matrix((a[,2:8])))
p.adjust(b, "BH")
Analyte -0.5-8 -0.5-12 -0.5-24 -0.5-168 8-12 12-24
24-168
1_1 0.98 0.31 0.71 0.73 0.54 0.08 0.02
2_1 0.51 0.03 0.65 0.64 0.18 0.02 0.90
3_1 0.92 0.18 0.49 0.93 0.12 0.04 0.37
4_1 0.18 0.52 0.86 0.17 0.68 0.68 0.67
5_1 0.20 0.59 0.05 0.61 0.24 0.02 0.17
6_1 0.86 0.92 0.83 0.23 0.74 0.92 0.97
7_1 0.86 0.28 0.04 0.58 0.20 0.00 0.08
8 0.00 0.05 0.10 0.90 0.98 0.95 0.21
9 0.00 0.03 0.04 0.37 0.77 0.86 0.18
10 0.00 0.07 0.10 0.90 1.00 0.98 0.18
11 0.05 0.04 0.14 0.14 0.74 0.86 0.87
12 0.00 0.31 0.07 0.09 0.02 0.28 0.00
13 0.80 0.42 0.98 0.09 0.21 0.42 0.04
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[R] please help, iteration through a list of files and plot each one
I have many files in 1 directory, file names end in .txt.
Each file has 2 columns
col1 col2
2 3
3 4
4 5
5 6
I want to make a list of the file names and iterate through each plotting them
in a separate file $filename\.png with the png swapped for txt.
So far I have this, can someone help fill in the blanks?
Thank You!
file_list <- list.files()
for (file in file_list){
if (!exists("dataset")){
dataset <- read.table(file, header=TRUE, sep="\t")
}
if (exists("dataset")){
temp_dataset <-read.table(file, header=TRUE, sep="\t")
##how to plot(temp_dataset) each file and save png(file\.png)
}
}
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[R] Help Please, ggplot2
library(ggplot2)
a<- read.table("data", header=T)
b = na.omit(a)
ggplot(data=b) + geom_line(aes(x=timepoint, y=value,group=sample, colour=
factor(sample))) + geom_point(aes(x=timepoint, y=value, group=s
ample)) + facet_wrap(~bio, scales = "free",ncol = 5) +theme_bw() +
opts(legend.direction = "horizontal", legend.position = "top",
legend.background = theme_blank()) + labs(fill="")
dev.off()
This generates one nice plot with many many plots in 1 file.
How do I modify the code to split up the plots into single file instead of
merging them in 1 file I want each plot to be in a separate file ?
Thanks in advance
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[R] Please help....normalization by the median of some control genes
Can someone show me some code to do normalization by the median of some control genes for the example below? Many Many Thanks in advance This strategy selects a subset of genes (called “control genes”) and makes the median of their data distribution similar across arrays. id1 id2 id3 control1 0.8 0.7 0.6 control2 0.6 0.2 0.4 probe1 0.3 0.2 0.5 probe2 0.4 0.9 0.7 probe3 0.6 0.7 0.4 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] qplot and colors (Please Help)
Please help:
I am using qplot as below and want to specify a different color scheme for race
but dont know how, can someone show me.
Thanks in advance
Code and input file below:
library(ggplot2)
library(gridExtra)
d<-read.table("results", header=TRUE, fill=TRUE)
plot2<-qplot(X,Y,data=d,color=race,facets=TYPE~., xlab="X", ylab="Y") +
theme_bw()
grid.arrange(plot2,ncol=1)
dev.off()
cat results
X Y ID race TYPE
0.0350 0.0200 1 X NA
0.0280 0.0251 2 X NA
0.0258 0.01753 Y NA
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Re: [R] Re : image.plot specify colors for range of data points, please help
Thank you so much!
- Original Message -
From: Pascal Oettli
To: David Lyon
Cc: "r-help@r-project.org"
Sent: Tuesday, April 17, 2012 11:31 AM
Subject: Re : [R] image.plot specify colors for range of data points, please
help
Hi,
> image.plot(x, breaks=c(-100,-1,1,100), col=c('green','black','red'))
Regards,
Pascal
- Mail original -
De : David Lyon
À : "r-help@r-project.org"
Cc :
Envoyé le : Mercredi 18 avril 2012 0h00
Objet : [R] image.plot specify colors for range of data points, please help
Hi
If I had a dataset of the following below and I want to plot colors for this
image.plot so that:
red for data above 1
black for data between/equal 1 and -1
green for data below -1
normally its:
image.plot(data) but how do I add the colors for the range of data points as
above?
Many thanks for your help!
_DATA_
2.04
2.02
1.60
1.92
0.98
0.50
0.40
-0.50
-0.40
-1.90
-2.8
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[R] image.plot specify colors for range of data points, please help
Hi If I had a dataset of the following below and I want to plot colors for this image.plot so that: red for data above 1 black for data between/equal 1 and -1 green for data below -1 normally its: image.plot(data) but how do I add the colors for the range of data points as above? Many thanks for your help! _DATA_ 2.04 2.02 1.60 1.92 0.98 0.50 0.40 -0.50 -0.40 -1.90 -2.8 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] image.plot adding x-axis labels. Please Help
Sorry that didnt work for me, any ideas?
- Original Message -
From: ilai
To: David Lyon
Cc: "r-help@r-project.org"
Sent: Tuesday, April 3, 2012 10:43 PM
Subject: Re: [R] image.plot adding x-axis labels. Please Help
On Tue, Apr 3, 2012 at 7:25 PM, David Lyon wrote:
> if I had a data file like this:
> 1.42 1.29 -0.13
> 1.46 1.34 -0.12
> 1.45 1.32 -0.13
> 1.36 1.26 -0.10
> 1.33 1.29 -0.04
>
> I want to create a image plot like this:
> data1<-read.table("A")
>
> image.plot(t(data1), axes=FALSE, xlab=NA, ylab=NA)
>
> I cant get the labels for the x axis right can some kind person help me?
axis(1,at=seq(0,1,l=ncol(data1)),labels=LETTERS[1:ncol(data1)])
> axis(1.???.labels=c("A", "B", "C"))
>
>
> Many thanks in advance!
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
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[R] image.plot adding x-axis labels. Please Help
if I had a data file like this:
1.42 1.29 -0.13
1.46 1.34 -0.12
1.45 1.32 -0.13
1.36 1.26 -0.10
1.33 1.29 -0.04
I want to create a image plot like this:
data1<-read.table("A")
image.plot(t(data1), axes=FALSE, xlab=NA, ylab=NA)
I cant get the labels for the x axis right can some kind person help me?
axis(1.???.labels=c("A", "B", "C"))
Many thanks in advance!
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[R] dot chart adding group labels....HELP
HI everyone
Does anayone know how to add group labels to dot charts
>From the R code below
a<-read.table("test2", sep="\t", header=TRUE)
dotchart(as.matrix(t()), main="test")
it generates from the datafile input below,
file test2 containing:
A B C D E
1 1 1 1 0.2068594
1 0.2386699 1 1 0.3959740
1 0.3965243 1 1 1.000
1 1.000 1 1 0.3329179
1 1.000 1 1 0.4873605
It gives by default the group labels "1","2","3","4" and "5"
How do I change the group labels from the default "1","2","3","4" and "5" to
something more useful say "place1","place2", "place3", "place4", "place5"
A BIG thanks in advance!
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Re: [R] Please help......barplot2
Thanks David Do you have the url link that details the worked solution to my problem: "that we have an extensive collection of documentation suitable for beginners that probably has similar problems worked out:" If not can someone show me how to " How do I import the file, then plot the mean and standard error bars of the data from each row?" Thanks in advance. Also this is not an homework problem just somebody using it as a newbie at work in research who normally codes in C, C++ and JAVA. Thanks again. --- On Thu, 12/2/10, David Winsemius wrote: > From: David Winsemius > Subject: Re: [R] Please help..barplot2 > To: "David Lyon" > Cc: r-help@r-project.org > Date: Thursday, December 2, 2010, 10:57 AM > > On Dec 2, 2010, at 10:36 AM, David Lyon wrote: > > > Hi everyone > > > > I spent hours trying to figure this out but as a > newbie I am stuck... > > can someone show me the R code for the following: > > > > If I had a tab delimited file called "file", > > Are you sure that you are not on an OS that hides the file > extensions by default? > > > > containing 3 rows : > > 9.56 8.67 > 9.28 8.81 > 7.93 9.85 > 8.92 10.19 > 8.63 > > 6.36 7.29 > 6.68 7.11 > 8.04 6.05 > 7.04 5.80 > 7.34 > > 3.22 3.22 > 3.28 4.37 > 5.21 3.10 > 3.37 2.56 > 5.43 > > > > How do I import the file, then plot the mean and > standard error bars of the data from each row? > > If the files name is really "file" then: > > read.table(file="file", header=FALSE, sep="\t") > > At this point I will note that this appears to be > structured along the lines I might except for a homework > problem. I will offer the advice that the plotCI function in > package plotrix looks suitable and that we have an extensive > collection of documentation suitable for beginners that > probably has similar problems worked out: > > > > > > > > Thank you so much > > > > __ > > R-help@r-project.org > mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, > reproducible code. > > David Winsemius, MD > West Hartford, CT > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Please help......barplot2
Hi everyone I spent hours trying to figure this out but as a newbie I am stuck... can someone show me the R code for the following: If I had a tab delimited file called "file", containing 3 rows : 9.568.679.288.817.939.858.9210.19 8.63 6.367.296.687.118.046.057.045.807.34 3.223.223.284.375.213.103.372.565.43 How do I import the file, then plot the mean and standard error bars of the data from each row? Thank you so much __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
