scatter plot with std error

Question

Hello everyone specially all R programmer, I need your kind help. I am trying to make scatter plot with std error bar![enter image description here][1] but i couldn't manage it. Till now I can make scatter plot with labels and 45 degree angle line(which I need also). If anyone help me or add some code in my existing one that will be very much helpful for me.

My code

Dataset <- read.table("AvgDis.csv",header=TRUE, sep="", 
                      na.strings="NA", dec=".", 
                      strip.white=TRUE)

plot(Dataset$True,Dataset$False, 
     xlim=c(0,100), ylim=c(0,100), 
     main="Average % of disorder", 
     xlab="True", ylab="False", 
     pch=19,col= "blue")

text(Dataset$True,Dataset$False, 
     labels=Dataset$MotifId, 
     cex= 0.7, pos=3)

abline(0,1)

Data, I am using :

   False        True     MotifId
54.1666675    33.33333    aps
35.2040825    48.57143    dbox
44.3055575    94.44444    ken
70.37037      60          mdm2
1.6666675      0          met
72.222225    100          ptk
46.9212975    68.51852    scftrcp1
55.5555575    70.83333    siah

Answer 1

First I'm going to create a fake data frame, because the way you've posted your data makes it inconvenient to copy and paste.

# Make a fake dataset since it is inconvenient to copy & paste the data you show
set.seed(13)
False <- rnorm(10, mean=50, sd=10)
True <- rnorm(10, mean=50, sd=10)
MotifId <- letters[1:10]
Dataset <- data.frame(False, True, MotifId)

You'll need to calculate the standard error somehow. Let's just imagine that all the data points have the same standard error:

Dataset$stderr <- 7 # This will recycle to the number of rows of Dataset

Now create your plot and add error bars as arrow s, as suggested here

plot(Dataset$True,Dataset$False, 
     xlim=c(0,100), ylim=c(0,100), 
     main="Average % of disorder", 
     xlab="True", ylab="False", 
     pch=19,col= "blue")
text(Dataset$True,Dataset$False, 
     labels=Dataset$MotifId, 
     cex= 0.7, pos=3)
abline(0,1)
arrows(x0=Dataset$True, y0=Dataset$False - Dataset$stderr, 
       x1=Dataset$True, y1=Dataset$False + Dataset$stderr, 
       angle=90, code=3, length=0.05)

In the long term I think it is preferable to use the ggplot2 data visualization package

require(ggplot2)
# Build the plot from layers 
p <- ggplot(Dataset, aes(x=True, y=False, label=MotifId)) + 
       geom_point() + 
       geom_text(, vjust=1, hjust=1) +
       geom_errorbar(aes(ymin=False-stderr, ymax=False+stderr), width=1) +
       geom_abline(slope=1, intercept=0) +
       xlim(c(0, 100)) +
       ylim(c(0, 100)) +
       ggtitle("Average % of disorder") +
       theme_bw()
print(p)