[R] y axis in a stacked bar plot

[Michelle Simon]

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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