Loren
2015-Mar-24 22:40 UTC
[R] facets work in qplot but facet_wrap produces an error in ggplot
Hello all,
I am having a perplexing problem trying to use facet_wrap in ggplot, with
both my real dataset and a simplified dummy dataset. I am trying to plot
heterozygosity across the genome for multiple individuals, with each
chromosome shown separately.
My dummy data:
chr1 123000 124000 2 0.00002 26 0.00026 indiv1
chr1 124000 125000 3 0.00003 12 0.00012 indiv1
chr1 125000 126000 1 0.00001 6 0.00006 indiv1
chr1 126000 126000 2 0.00002 14 0.00014 indiv1
chr2 123000 124000 6 0.00006 20 0.00020 indiv1
chr2 124000 125000 0 0.00000 12 0.00012 indiv1
chr1 123000 124000 2 0.00002 26 0.00026 indiv2
chr1 124000 125000 3 0.00003 12 0.00012 indiv2
chr1 125000 126000 1 0.00001 6 0.00006 indiv2
chr1 126000 126000 2 0.00002 14 0.00014 indiv2
chr2 123000 124000 6 0.00006 20 0.00020 indiv2
chr2 124000 125000 0 0.00000 12 0.00012 indiv2
My code to read in the data:
hetshoms <- read.table("fakedata.txt", header=F)
chrom <- hetshoms$V1
start.pos <- hetshoms$V2
end.pos <- hetshoms$V3
hets <- hetshoms$V4
het_stat <- hetshoms$V5
homs <- hetshoms$V6
hom_stat <- hetshoms$V7
indiv <- hetshoms$V8
HetRatio <- hets/(hets+homs)
When I try to plot the chromosomes separately in qplot, it works fine:
testplot <- qplot(start.pos, HetRatio, facets = chrom ~ ., colour=chrom)
But when I try an analogous thing in ggplot, it does not work.
The first part works fine:
testplot <- ggplot(hetshoms, aes(x=start.pos, y=HetRatio)) +
geom_point(aes(color=chrom, alpha=1/4))
but when I try to add the facet_wrap:
testplot + facet_wrap(~chrom)
This produces the following error (and no plot)
"Error en layout_base(data, vars, drop = drop) :
At least one layer must contain all variables used for facetting"
I have tried adding an (as.formula(paste)) and directly calling hetshoms$V1
but neither solves the problem.
Can anyone please point out where I have gone wrong and how to fix my code?
Much appreciated,
Loren
--
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Jeff Newmiller
2015-Mar-25 03:19 UTC
[R] facets work in qplot but facet_wrap produces an error in ggplot
You MUST put all data you plan to refer to into a data frame when using ggplot.
There are a couple of ways you could do this... the easiest is to put a header
line in the data file with column names. Or, you can assign a vector of new
names to the names of the data frame.
names( hetshoms ) <- c( "chrom", "start.pos",
"end.pos", "hets", "het_stat", "homs",
"hom_stat", "indiv" )
---------------------------------------------------------------------------
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Sent from my phone. Please excuse my brevity.
On March 24, 2015 3:40:11 PM PDT, Loren <sackettl at colorado.edu>
wrote:>Hello all,
>
>I am having a perplexing problem trying to use facet_wrap in ggplot,
>with
>both my real dataset and a simplified dummy dataset. I am trying to
>plot
>heterozygosity across the genome for multiple individuals, with each
>chromosome shown separately.
>
>My dummy data:
>chr1 123000 124000 2 0.00002 26 0.00026 indiv1
>chr1 124000 125000 3 0.00003 12 0.00012 indiv1
>chr1 125000 126000 1 0.00001 6 0.00006 indiv1
>chr1 126000 126000 2 0.00002 14 0.00014 indiv1
>chr2 123000 124000 6 0.00006 20 0.00020 indiv1
>chr2 124000 125000 0 0.00000 12 0.00012 indiv1
>chr1 123000 124000 2 0.00002 26 0.00026 indiv2
>chr1 124000 125000 3 0.00003 12 0.00012 indiv2
>chr1 125000 126000 1 0.00001 6 0.00006 indiv2
>chr1 126000 126000 2 0.00002 14 0.00014 indiv2
>chr2 123000 124000 6 0.00006 20 0.00020 indiv2
>chr2 124000 125000 0 0.00000 12 0.00012 indiv2
>
>My code to read in the data:
>hetshoms <- read.table("fakedata.txt", header=F)
>
>chrom <- hetshoms$V1
>start.pos <- hetshoms$V2
>end.pos <- hetshoms$V3
>hets <- hetshoms$V4
>het_stat <- hetshoms$V5
>homs <- hetshoms$V6
>hom_stat <- hetshoms$V7
>indiv <- hetshoms$V8
>
>HetRatio <- hets/(hets+homs)
>
>When I try to plot the chromosomes separately in qplot, it works fine:
>testplot <- qplot(start.pos, HetRatio, facets = chrom ~ .,
>colour=chrom)
>
>But when I try an analogous thing in ggplot, it does not work.
>The first part works fine:
>testplot <- ggplot(hetshoms, aes(x=start.pos, y=HetRatio)) +
>geom_point(aes(color=chrom, alpha=1/4))
>
>but when I try to add the facet_wrap:
>testplot + facet_wrap(~chrom)
>
>This produces the following error (and no plot)
>"Error en layout_base(data, vars, drop = drop) :
> At least one layer must contain all variables used for facetting"
>
>I have tried adding an (as.formula(paste)) and directly calling
>hetshoms$V1
>but neither solves the problem.
>
>Can anyone please point out where I have gone wrong and how to fix my
>code?
>
>Much appreciated,
>Loren
>
>
>
>
>
>
>--
>View this message in context:
>http://r.789695.n4.nabble.com/facets-work-in-qplot-but-facet-wrap-produces-an-error-in-ggplot-tp4705058.html
>Sent from the R help mailing list archive at Nabble.com.
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>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.
Loren Cassin Sackett
2015-Mar-25 13:49 UTC
[R] facets work in qplot but facet_wrap produces an error in ggplot
Thanks, Jeff. I tried this previously by using a header in my data file (and 'header=TRUE'), but for some reason, that did not seem to work. Creating a 'names' vector as you suggested did solve the problem, though. Thank you! Loren 2015-03-24 23:19 GMT-04:00 Jeff Newmiller <jdnewmil at dcn.davis.ca.us>:> You MUST put all data you plan to refer to into a data frame when using > ggplot. There are a couple of ways you could do this... the easiest is to > put a header line in the data file with column names. Or, you can assign a > vector of new names to the names of the data frame. > > names( hetshoms ) <- c( "chrom", "start.pos", "end.pos", "hets", > "het_stat", "homs", "hom_stat", "indiv" ) > --------------------------------------------------------------------------- > Jeff Newmiller The ..... ..... Go Live... > DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live > Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/Batteries O.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > --------------------------------------------------------------------------- > Sent from my phone. Please excuse my brevity. > > On March 24, 2015 3:40:11 PM PDT, Loren <sackettl at colorado.edu> wrote: > >Hello all, > > > >I am having a perplexing problem trying to use facet_wrap in ggplot, > >with > >both my real dataset and a simplified dummy dataset. I am trying to > >plot > >heterozygosity across the genome for multiple individuals, with each > >chromosome shown separately. > > > >My dummy data: > >chr1 123000 124000 2 0.00002 26 0.00026 indiv1 > >chr1 124000 125000 3 0.00003 12 0.00012 indiv1 > >chr1 125000 126000 1 0.00001 6 0.00006 indiv1 > >chr1 126000 126000 2 0.00002 14 0.00014 indiv1 > >chr2 123000 124000 6 0.00006 20 0.00020 indiv1 > >chr2 124000 125000 0 0.00000 12 0.00012 indiv1 > >chr1 123000 124000 2 0.00002 26 0.00026 indiv2 > >chr1 124000 125000 3 0.00003 12 0.00012 indiv2 > >chr1 125000 126000 1 0.00001 6 0.00006 indiv2 > >chr1 126000 126000 2 0.00002 14 0.00014 indiv2 > >chr2 123000 124000 6 0.00006 20 0.00020 indiv2 > >chr2 124000 125000 0 0.00000 12 0.00012 indiv2 > > > >My code to read in the data: > >hetshoms <- read.table("fakedata.txt", header=F) > > > >chrom <- hetshoms$V1 > >start.pos <- hetshoms$V2 > >end.pos <- hetshoms$V3 > >hets <- hetshoms$V4 > >het_stat <- hetshoms$V5 > >homs <- hetshoms$V6 > >hom_stat <- hetshoms$V7 > >indiv <- hetshoms$V8 > > > >HetRatio <- hets/(hets+homs) > > > >When I try to plot the chromosomes separately in qplot, it works fine: > >testplot <- qplot(start.pos, HetRatio, facets = chrom ~ ., > >colour=chrom) > > > >But when I try an analogous thing in ggplot, it does not work. > >The first part works fine: > >testplot <- ggplot(hetshoms, aes(x=start.pos, y=HetRatio)) + > >geom_point(aes(color=chrom, alpha=1/4)) > > > >but when I try to add the facet_wrap: > >testplot + facet_wrap(~chrom) > > > >This produces the following error (and no plot) > >"Error en layout_base(data, vars, drop = drop) : > > At least one layer must contain all variables used for facetting" > > > >I have tried adding an (as.formula(paste)) and directly calling > >hetshoms$V1 > >but neither solves the problem. > > > >Can anyone please point out where I have gone wrong and how to fix my > >code? > > > >Much appreciated, > >Loren > > > > > > > > > > > > > >-- > >View this message in context: > > > http://r.789695.n4.nabble.com/facets-work-in-qplot-but-facet-wrap-produces-an-error-in-ggplot-tp4705058.html > >Sent from the R help mailing list archive at Nabble.com. > > > >______________________________________________ > >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >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. > >[[alternative HTML version deleted]]