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Question

I want to have a straight line plot of intensity values for 10 different molecules with molecule name on the x axis and intensity value on the y axis.

I tried:

x = c("Mol 1","Mol 2","Mol 3","Mol 4","Mol 5","Mol 6","Mol 7","Mol 8","Mol 9","Mol 10")
intensity = c(428,409,388,378,373,140,137,138,139,144)
plot(x,intensity)

But it returned this error message?

Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion 2: In min(x) : no non-missing arguments to min; returning Inf 3: In max(x) : no non-missing arguments to max; returning -Inf

Answer 1

Because your x variable is discrete, you need to do this a little differently:

plot(seq_along(x),intensity,type = "l",axes = FALSE)
axis(side = 2)
axis(side = 1,at = seq_along(x),labels = x)

The idea being that you create the plot with numerical values for the x axis, and then simply add your particular labels.

You can add a call to box() if you miss the full box around the plot.

Answer 2

You can do this by making your "x" a factor.

xFact<-factor(x, levels=x)
plot.default(xFact,intensity)

Edited to change plot to plot.default . As Joran points out, if you just use plot you get a boxplot.

Re-edit: To get the x axis to display the proper labels use:

plot.default(xFact,intensity,type="p",xaxt="n")
axis(side=1, at=xFact,labels=x)

Answer 3

Using ggplot:

library(ggplot2)
df <- data.frame(id=1:length(x),x,intensity)
ggplot(df)+                               # set default dataset
  geom_point(aes(x=id,y=intensity))+      # plot the points
  scale_x_discrete(labels=x)+             # label the x-axis ticks
  labs(x="Molecule")+                     # label the x axis
  theme(axis.text.x=element_text(angle=90,vjust=.2,hjust=1))  # rotate and align tick labels