Greetings, I am new to R, but trying to put in the time to learn. I have read the R manual and several other introductory texts; however, there is nothing like actually putting it into practice. So here is my problem, and its more of a learning exercise for myself than anything else, but I'm stuck and getting extremely frustrated that I can't figure it out. I'm trying to make a fairly simple figure, but also trying to make it look "better" using ggplot2. I have data.frame that contains chrom length 1 chr1 249250621 2 chr2 243199373 3 chr3 198022430 4 chr4 191154276 5 chr5 180915260 6 chr6 171115067 7 chr7 159138663 8 chrX 155270560 9 chr8 146364022 10 chr9 141213431 11 chr10 135534747 12 chr11 135006516 13 chr12 133851895 14 chr13 115169878 15 chr14 107349540 16 chr15 102531392 17 chr16 90354753 18 chr17 81195210 19 chr18 78077248 20 chr20 63025520 21 chrY 59373566 22 chr19 59128983 23 chr22 51304566 24 chr21 48129895 I want to drop the "chr" and order the chrom column in ascending order with X & Y at the end. I have tried converting the chrom into a character vector and using the strsplit function, but then I have to circle back and do a lot of editing to make it work. I could do this in excel or some other program, but again I'm really trying to learn R and if I had to do something 100 times working in R would be so much better. I did however write the above to an excel spreadsheet and did the simple edits I need to make a bar chart. Using bar plot I was able to make a nice simple figure, but it isn't necessarily as aesthetically pleasing as the figures made in ggplot2 or other packages. So when I made the same figure in ggplot2 it worked, but reordered the chrom column as 1, 10, 11, 12......X,Y. I figured out this is because the package orders things in an a-b-c type of fashion. I could resort the column as a factors and manually define the levels, but again I'm trying to learn R and make it work more efficiently for my purposes in the future. Could someone help me understand how I could accomplishing taking the above data.frame, splitting it / dropping chr, ordering it, and then graphing it? Thank you in advance for your help. I've tried working on this for the past day and a half but can't figure it out, and the learning phase is really costing me in terms of being productive. [[alternative HTML version deleted]]
??
ggplot did not reorder the columns -- it just plotted them in the order of
the levels of factor(chrom), which is exactly what you wanted afaics. There
is no need to reorder to do what you want.
Comment: ?dput to put reproducible data into an email that people can
conveniently copy and paste into R.
However, if you wish to do so: (untested since you did not use dput)
Assume your data.frame is named df
1. First change chrom into a character column:
chrm <- as.character(df$chrom)
2. Use regular expressions to get rid of the chr.
df$chrom <- sub("chr","",chrm)
3. Use ?order to reorder (since the default ordering is what you want at
least in English locales)
chrom <- chrom[order(df$chrom,]
Does this give you what you wanted?
-- Bert
On Thu, Jun 21, 2012 at 9:33 AM, Kevin Parrish <kparrish0@gmail.com>
wrote:
> Greetings,
>
> I am new to R, but trying to put in the time to learn. I have read the R
> manual and several other introductory texts; however, there is nothing like
> actually putting it into practice. So here is my problem, and its more of a
> learning exercise for myself than anything else, but I'm stuck and
getting
> extremely frustrated that I can't figure it out.
>
> I'm trying to make a fairly simple figure, but also trying to make it
look
> "better" using ggplot2.
>
> I have data.frame that contains
>
> chrom length
>
> 1 chr1 249250621
>
> 2 chr2 243199373
>
> 3 chr3 198022430
>
> 4 chr4 191154276
>
> 5 chr5 180915260
>
> 6 chr6 171115067
>
> 7 chr7 159138663
>
> 8 chrX 155270560
>
> 9 chr8 146364022
>
> 10 chr9 141213431
>
> 11 chr10 135534747
>
> 12 chr11 135006516
>
> 13 chr12 133851895
>
> 14 chr13 115169878
>
> 15 chr14 107349540
>
> 16 chr15 102531392
>
> 17 chr16 90354753
>
> 18 chr17 81195210
>
> 19 chr18 78077248
>
> 20 chr20 63025520
>
> 21 chrY 59373566
>
> 22 chr19 59128983
>
> 23 chr22 51304566
>
> 24 chr21 48129895
>
>
> I want to drop the "chr" and order the chrom column in ascending
order with
> X & Y at the end.
>
> I have tried converting the chrom into a character vector and using the
> strsplit function, but then I have to circle back and do a lot of editing
> to make it work.
>
> I could do this in excel or some other program, but again I'm really
trying
> to learn R and if I had to do something 100 times working in R would be so
> much better. I did however write the above to an excel spreadsheet and did
> the simple edits I need to make a bar chart. Using bar plot I was able to
> make a nice simple figure, but it isn't necessarily as aesthetically
> pleasing as the figures made in ggplot2 or other packages. So when I made
> the same figure in ggplot2 it worked, but reordered the chrom column as 1,
> 10, 11, 12......X,Y. I figured out this is because the package orders
> things in an a-b-c type of fashion. I could resort the column as a factors
> and manually define the levels, but again I'm trying to learn R and
make it
> work more efficiently for my purposes in the future.
>
>
> Could someone help me understand how I could accomplishing taking the above
> data.frame, splitting it / dropping chr, ordering it, and then graphing it?
>
>
> Thank you in advance for your help. I've tried working on this for the
past
> day and a half but can't figure it out, and the learning phase is
really
> costing me in terms of being productive.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
[[alternative HTML version deleted]]
Hello,
Try the following.
dd <- read.table(text="
chrom length
1 chr1 249250621
2 chr2 243199373
[... etc ...]
22 chr19 59128983
23 chr22 51304566
24 chr21 48129895
", header=TRUE)
str(dd)
dd$chrom <- as.character(dd$chrom)
dd$chrom <- sub("chr", "", dd$chrom)
# This 'chrom' is NOT a data.frame column
chrom <- dd$chrom
chrom[chrom == "X"] <- 100 # bigger than any dd$chrom
chrom[chrom == "Y"] <- 200 # bigger than for dd$chrom ==
"X"
chrom <- as.integer(chrom)
ord <- order(chrom)
barplot(dd$length[ord], names.arg=dd$chrom[ord])
Note that it uses base graphics. Do you really need ggplot2? If the goal
is to make it prettier but it wasn't working, you still don't know where
you can go with the simpler...
Hope this helps,
Rui Barradas
Em 21-06-2012 17:33, Kevin Parrish escreveu:> Greetings,
>
> I am new to R, but trying to put in the time to learn. I have read the R
> manual and several other introductory texts; however, there is nothing like
> actually putting it into practice. So here is my problem, and its more of a
> learning exercise for myself than anything else, but I'm stuck and
getting
> extremely frustrated that I can't figure it out.
>
> I'm trying to make a fairly simple figure, but also trying to make it
look
> "better" using ggplot2.
>
> I have data.frame that contains
>
> chrom length
>
> 1 chr1 249250621
>
> 2 chr2 243199373
>
> 3 chr3 198022430
>
> 4 chr4 191154276
>
> 5 chr5 180915260
>
> 6 chr6 171115067
>
> 7 chr7 159138663
>
> 8 chrX 155270560
>
> 9 chr8 146364022
>
> 10 chr9 141213431
>
> 11 chr10 135534747
>
> 12 chr11 135006516
>
> 13 chr12 133851895
>
> 14 chr13 115169878
>
> 15 chr14 107349540
>
> 16 chr15 102531392
>
> 17 chr16 90354753
>
> 18 chr17 81195210
>
> 19 chr18 78077248
>
> 20 chr20 63025520
>
> 21 chrY 59373566
>
> 22 chr19 59128983
>
> 23 chr22 51304566
>
> 24 chr21 48129895
>
>
> I want to drop the "chr" and order the chrom column in ascending
order with
> X & Y at the end.
>
> I have tried converting the chrom into a character vector and using the
> strsplit function, but then I have to circle back and do a lot of editing
> to make it work.
>
> I could do this in excel or some other program, but again I'm really
trying
> to learn R and if I had to do something 100 times working in R would be so
> much better. I did however write the above to an excel spreadsheet and did
> the simple edits I need to make a bar chart. Using bar plot I was able to
> make a nice simple figure, but it isn't necessarily as aesthetically
> pleasing as the figures made in ggplot2 or other packages. So when I made
> the same figure in ggplot2 it worked, but reordered the chrom column as 1,
> 10, 11, 12......X,Y. I figured out this is because the package orders
> things in an a-b-c type of fashion. I could resort the column as a factors
> and manually define the levels, but again I'm trying to learn R and
make it
> work more efficiently for my purposes in the future.
>
>
> Could someone help me understand how I could accomplishing taking the above
> data.frame, splitting it / dropping chr, ordering it, and then graphing it?
>
>
> Thank you in advance for your help. I've tried working on this for the
past
> day and a half but can't figure it out, and the learning phase is
really
> costing me in terms of being productive.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.
>