Your data has commas in the numbers causing them to be read in as factors:
> x <- read.table(textConnection(" ID Cn read_count
+ 1 MJ-2000-79 10,000 6876
+ 2 MJ-2000-80 10,000 23440
+ 3 MJ-2000-87 10,000 18787
+ 4 MJ-2000-100 8000 4775
+ 5 MJ-2000-81 8000 1542
+ 6 MJ-2000-82 8000 1550
+ 7 MJ-2000-101 6000 15322
+ 8 MJ-2000-83 6000 7023
+ 9 MJ-2000-84 6000 834
+ 10 MJ-2000-102 4000 4216
+ 11 MJ-2000-85 4000 1174
+ 12 MJ-2000-86 4000 404
+ 13 MJ-4000-131 1000 1368
+ 14 MJ-4000-132 1000 2219
+ 15 MJ-4000-125 800 413
+ 16 MJ-4000-133 800 2594
+ 17 MJ-4000-127 600 3059
+ 18 MJ-4000-134 600 1561
+ 19 MJ-4000-142 600 848
+ 20 MJ-4000-129 400 182
+ 21 MJ-4000-130 400 1410
+ 22 MJ-4000-135 400 2713
+ 23 MJ-7000-182 100 943
+ 24 MJ-8000-184 100 318
+ 25 MJ-8000-185 80 92
+ 26 MJ-8000-186 80 161
+ 27 MJ-8000-188 60 158
+ 28 MJ-8000-191 60 103
+ 29 MJ-8000-192 40 468
+ 30 MJ-8000-193 40 432"), header=TRUE)
> str(x) # notice that the column is a factor; comma is not recognizable in
> numbers
'data.frame': 30 obs. of 3 variables:
$ ID : Factor w/ 30 levels "MJ-2000-100",..: 4 5 12 1 6 7 2 8 9 3 ...
$ Cn : Factor w/ 12 levels "10,000","100",..: 1 1 1 12 12 12 9 9 9 6 ...
$ read_count: int 6876 23440 18787 4775 1542 1550 15322 7023 834 4216 ...
> # remove the comma and convert to numeric
> x$Cn <- as.numeric(gsub(",", "", as.character(x$Cn)))
> str(x)
'data.frame': 30 obs. of 3 variables:
$ ID : Factor w/ 30 levels "MJ-2000-100",..: 4 5 12 1 6 7 2 8 9 3 ...
$ Cn : num 10000 10000 10000 8000 8000 8000 6000 6000 6000 4000 ...
$ read_count: int 6876 23440 18787 4775 1542 1550 15322 7023 834 4216 ...
> plot(x$Cn, x$read_count)
>
>
>
On Sat, Jul 18, 2009 at 6:18 PM, ANJAN
PURKAYASTHA<anjan.purkayas...@gmail.com> wrote:
> Hi I have a data set that needs to be plotted (see below)
> When I plot it using the simple plot(read_count ~ Cn), I get box plots for
> the read_count numbers plotted according to Cn. The Cn's on the x-axis are
> ordered: 10000, 100, 1000, 40, 400, 4000...
> How do I plot so that Cn is plotted on the x-axis in an ascending order: 40,
> 60, 80, .......10000?
>
> Thanks for your help.
> Anjan
>
>
> ID Cn read_count
> 1 MJ-2000-79 10,000 6876
> 2 MJ-2000-80 10,000 23440
> 3 MJ-2000-87 10,000 18787
> 4 MJ-2000-100 8000 4775
> 5 MJ-2000-81 8000 1542
> 6 MJ-2000-82 8000 1550
> 7 MJ-2000-101 6000 15322
> 8 MJ-2000-83 6000 7023
> 9 MJ-2000-84 6000 834
> 10 MJ-2000-102 4000 4216
> 11 MJ-2000-85 4000 1174
> 12 MJ-2000-86 4000 404
> 13 MJ-4000-131 1000 1368
> 14 MJ-4000-132 1000 2219
> 15 MJ-4000-125 800 413
> 16 MJ-4000-133 800 2594
> 17 MJ-4000-127 600 3059
> 18 MJ-4000-134 600 1561
> 19 MJ-4000-142 600 848
> 20 MJ-4000-129 400 182
> 21 MJ-4000-130 400 1410
> 22 MJ-4000-135 400 2713
> 23 MJ-7000-182 100 943
> 24 MJ-8000-184 100 318
> 25 MJ-8000-185 80 92
> 26 MJ-8000-186 80 161
> 27 MJ-8000-188 60 158
> 28 MJ-8000-191 60 103
> 29 MJ-8000-192 40 468
> 30 MJ-8000-193 40 432
>
> --
> =============================
> anjan purkayastha, phd
> bioinformatics analyst
> whitehead institute for biomedical research
> nine cambridge center
> cambridge, ma 02142
>
> purkayas [at] wi [dot] mit [dot] edu
> 703.740.6939
>
> [[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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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