在R中创建包含3个变量的图

Question

I had been following the analysis steps in the Little Book of R . It is a great tutorial but for things to work, it and many other tutorials need to have the data organized a certain way.

My data is structured like this (a very tiny tiny sample)a:

Phylum Confidence Time Seq_ID Environment Dataset
Acidobacteria 0.801 5 >3134898 Marine 4440037.3
Bacteroidetes 0.812 6 >3066473 Marine 4440037.3
Acidobacteria 0.828 5 >3085551 Gut 4440038.3
Firmicutes    0.830 4 >3087676 Coral 4440036.3

I want a good way to

a) Plot the Time by bacterial phylum for each environment. I realize that this means I will need to created a plot for each phylum. (see plots )

b. Plot the time by environment of two different phyla which I will then color code by environment. (see plots )

I know I can create a new dataframe based on an environment and bacteria, but I have not been able to incorporate it correctly into a plot that uses a third variable (time).

new_df = myDF[(myDF$Environment=='Marine') & (myDF$Phylum=='Acidobacteria'),]

I have tried several things...

p <- ggplot(myDF, aes(Environment, Time))
p + geom_boxplot(aes(fill = Environment))

It creates a plot, but this does not take into consideration the phylum (eg I would like a separate plot for each phylum).

Or this...

 for (i in environment) #this is a list I created
 {
     for (j in phyla) #this is a list I created
     {
        #stats_df = myDF[(myDF$Environment==i) & (myDF$Phylum==j),]
        plot(myDF[[j]], myDF[[i]], xlab=NULL, ylab='Time')
      }
 }

This one gets errors

Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted

shell returned 1

But even if it did plot, it still does not take into consideration the Time variable. What I am really trying to figure out is how to use three variables in a plot.

Answer 1

Assuming phylum is a factor variable

library(ggplot2)
g<- ggplot(myDF, aes(Environment, Time))
g + geom_point() + facet_grid(. ~ phylum)

 library(ggplot2)

 g<- ggplot(df1, aes(Environment, Time))
 g + geom_point() + facet_grid(phylum ~ .)

Please see here for the details.