Hello,
Below is some simple R code I have used to create a stacked bar chart. However
the y-axis tick marks do not reflect the data. The minimum and maximum data
values I have are 3073351 and 25329814 respectively but the graph has data from
0 and the maximum is different The data file is too large so there is a small
sample below. What am I doing wrong? Please help as I cannot be sure the data
is represented correctly in the graph (attached).
fn <-"~/Documents/chr7Data.txt"
x<-read.table(fn,check.names = TRUE, header=T)
d <- data.frame(x)
theChart<-ggplot(d, aes(x=factor(Congenic),y=Position, fill=Strain,
theme_rect="white")) + geom_bar(stat='identity', position =
"stack" ) + scale_fill_manual(values=c("deepskyblue1",
"red2", "green3", "steelblue4",
"lightblue4", "gray70")) + ylab(c("Position"))+
ggtitle("Strain specific SNP distribution in the congenics") +
#coord_cartesian(ylim = c(min(d$Position), max(d$Position))) +
#scale_y_continuous(breaks=seq(0, 200000000, 50000000)) +
theme_bw()+
theme(plot.title = element_text(size=23),
axis.text.x = element_text(size=13, angle=90), #20 before
axis.text.y = element_text(size=13),
panel.border = element_rect(colour="BLACK",size=0.5),
axis.title.x = element_text(size=12),
axis.title.y = element_text(size=12,angle = 90),
panel.background = element_rect(fill="transparent"),
legend.text=element_text(size=13),
legend.title=element_text(size=12)
#plot.background = element_rect(fill =
"transparent",colour = NA)
)
png("~/Documents/sendToRGrp.png",950,750)
print(theChart)
dev.off()
??????????? Sample Data ?????????????
Congenic Position Strain
4201 3073351 hets
4203 3073351 reference
4215 3073351 reference
4333 3073351 cba
4335 3073351 cba
4484 3073351 cba
4485 3073351 reference
4496 3073351 hets
4497 3073351 reference
//lots of data//
4201 25329814 reference
4203 25329814 reference
4215 25329814 cba
4333 25329814 balbc
4335 25329814 balbc
4484 25329814 reference
4485 25329814 reference
4496 25329814 balbc
4497 25329814 hets
Many thanks,
Michy
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I don't understand what you expect. Stacked bar charts add the values
together. Perhaps that is not really how you want to represent these data?
---------------------------------------------------------------------------
Jeff Newmiller The ..... ..... Go Live...
DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live
Go...
Live: OO#.. Dead: OO#.. Playing
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---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.
On March 25, 2015 9:29:40 PM PDT, Michelle Simon <M.Simon at
har.mrc.ac.uk> wrote:>Hello,
>Below is some simple R code I have used to create a stacked bar chart.
>However the y-axis tick marks do not reflect the data. The minimum and
>maximum data values I have are 3073351 and 25329814 respectively but
>the graph has data from 0 and the maximum is different The data file
>is too large so there is a small sample below. What am I doing wrong?
>Please help as I cannot be sure the data is represented correctly in
>the graph (attached).
>
>fn <-"~/Documents/chr7Data.txt"
>x<-read.table(fn,check.names = TRUE, header=T)
>d <- data.frame(x)
>theChart<-ggplot(d, aes(x=factor(Congenic),y=Position, fill=Strain,
>theme_rect="white")) + geom_bar(stat='identity', position
= "stack" ) +
>scale_fill_manual(values=c("deepskyblue1", "red2",
"green3",
>"steelblue4", "lightblue4", "gray70")) +
ylab(c("Position"))+
>ggtitle("Strain specific SNP distribution in the congenics") +
>
>#coord_cartesian(ylim = c(min(d$Position), max(d$Position))) +
>#scale_y_continuous(breaks=seq(0, 200000000, 50000000)) +
>theme_bw()+
>theme(plot.title = element_text(size=23),
> axis.text.x = element_text(size=13, angle=90), #20 before
> axis.text.y = element_text(size=13),
> panel.border =
element_rect(colour="BLACK",size=0.5),
> axis.title.x = element_text(size=12),
> axis.title.y = element_text(size=12,angle = 90),
> panel.background =
element_rect(fill="transparent"),
> legend.text=element_text(size=13),
> legend.title=element_text(size=12)
> #plot.background = element_rect(fill = "transparent",colour
= NA)
>)
>png("~/Documents/sendToRGrp.png",950,750)
>print(theChart)
>dev.off()
>
>??????????? Sample Data ?????????????
>Congenic Position Strain
>4201 3073351 hets
>4203 3073351 reference
>4215 3073351 reference
>4333 3073351 cba
>4335 3073351 cba
>4484 3073351 cba
>4485 3073351 reference
>4496 3073351 hets
>4497 3073351 reference
>//lots of data//
>4201 25329814 reference
>4203 25329814 reference
>4215 25329814 cba
>4333 25329814 balbc
>4335 25329814 balbc
>4484 25329814 reference
>4485 25329814 reference
>4496 25329814 balbc
>4497 25329814 hets
>
>Many thanks,
>Michy
>
>
>This email may have a PROTECTIVE MARKING, for an explanation please
>see:
>http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
>
>
>------------------------------------------------------------------------
>
>______________________________________________
>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.
Hi Michy, I agree with Jeff that you probably don't want a stacked bar chart. What you describe appears to be a display of relative positions of genetic elements in different strains of mice and the place to ask is most likely the Bioconductor mailing list. Jim On Thu, Mar 26, 2015 at 3:51 PM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:> I don't understand what you expect. Stacked bar charts add the values > together. Perhaps that is not really how you want to represent these data? > --------------------------------------------------------------------------- > 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 25, 2015 9:29:40 PM PDT, Michelle Simon <M.Simon at har.mrc.ac.uk> > wrote: > >Hello, > >Below is some simple R code I have used to create a stacked bar chart. > >However the y-axis tick marks do not reflect the data. The minimum and > >maximum data values I have are 3073351 and 25329814 respectively but > >the graph has data from 0 and the maximum is different The data file > >is too large so there is a small sample below. What am I doing wrong? > >Please help as I cannot be sure the data is represented correctly in > >the graph (attached). > > > >fn <-"~/Documents/chr7Data.txt" > >x<-read.table(fn,check.names = TRUE, header=T) > >d <- data.frame(x) > >theChart<-ggplot(d, aes(x=factor(Congenic),y=Position, fill=Strain, > >theme_rect="white")) + geom_bar(stat='identity', position = "stack" ) + > >scale_fill_manual(values=c("deepskyblue1", "red2", "green3", > >"steelblue4", "lightblue4", "gray70")) + ylab(c("Position"))+ > >ggtitle("Strain specific SNP distribution in the congenics") + > > > >#coord_cartesian(ylim = c(min(d$Position), max(d$Position))) + > >#scale_y_continuous(breaks=seq(0, 200000000, 50000000)) + > >theme_bw()+ > >theme(plot.title = element_text(size=23), > > axis.text.x = element_text(size=13, angle=90), #20 before > > axis.text.y = element_text(size=13), > > panel.border = element_rect(colour="BLACK",size=0.5), > > axis.title.x = element_text(size=12), > > axis.title.y = element_text(size=12,angle = 90), > > panel.background = element_rect(fill="transparent"), > > legend.text=element_text(size=13), > > legend.title=element_text(size=12) > > #plot.background = element_rect(fill = "transparent",colour = NA) > >) > >png("~/Documents/sendToRGrp.png",950,750) > >print(theChart) > >dev.off() > > > >??????????? Sample Data ????????????? > >Congenic Position Strain > >4201 3073351 hets > >4203 3073351 reference > >4215 3073351 reference > >4333 3073351 cba > >4335 3073351 cba > >4484 3073351 cba > >4485 3073351 reference > >4496 3073351 hets > >4497 3073351 reference > >//lots of data// > >4201 25329814 reference > >4203 25329814 reference > >4215 25329814 cba > >4333 25329814 balbc > >4335 25329814 balbc > >4484 25329814 reference > >4485 25329814 reference > >4496 25329814 balbc > >4497 25329814 hets > > > >Many thanks, > >Michy > > > > > >This email may have a PROTECTIVE MARKING, for an explanation please > >see: > > > http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm > > > > > >------------------------------------------------------------------------ > > > >______________________________________________ > >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. > > ______________________________________________ > 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]]