Data Visualization In R

Question

[deschisandy]

The data to be visualized is from an experiment (T1-T8 represents different sections of the brain) and is as follows:

    [[Block1]]
              sum
       [T1,]   6
       [T2,]   6
       [T3,]   4
       [T4,]   5
       [T5,]   8
       [T6,]   9
       [T7,]   8
       [T8,]   6

    [[Block2]]
              sum
       [T1,]   3
       [T2,]   3
       [T3,]   4
       [T4,]   5
       [T5,]   4
       [T6,]   2
       [T7,]   1
       [T8,]   5

    [[Block3]]
              sum
       [T1,]   3
       [T2,]   3
       [T3,]   4
       [T4,]   2
       [T5,]   4
       [T6,]   8
       [T7,]   3
       [T8,]   1   

   [[Block4]]
              sum
       [T1,]   6
       [T2,]   5
       [T3,]   4
       [T4,]   3
       [T5,]   9
       [T6,]   8
       [T7,]   2
       [T8,]   6  

   [[Block5]]
              sum
       [T1,]   8
       [T2,]   3
       [T3,]   4
       [T4,]   5
       [T5,]   7
       [T6,]   6
       [T7,]   2
       [T8,]   2 

   [[Block6]]
              sum
       [T1,]   10
       [T2,]   9
       [T3,]   6
       [T4,]   8
       [T5,]   9
       [T6,]   4
       [T7,]   6
       [T8,]   7

and so on.. For more than 100 blocks..

I would like to visualize the data in the following way to see the overall value in each region for very block..

For one block I get a line plot as shown below:

But it is tedious to visualize the same for 100 blocks.. What would be the best method to view it as a single plot using R..I tried doing it with heat maps but I would rather visualize them as a graph..

In the end it should be something like ( I have a rough figure of it).. Iam not sure how to do this in R for several blocks in a single plot or some other better way to visualize it:

[Sukhi Singh]

Edit your question to a better title plus check facet_grid of ggplot!!

[bdemarest]

Cross-posted on stackoverflow, where several good answers have been offered. http://stackoverflow.com/questions/17280468/data-visualization-in-r

Answer 1

[Giovanni M Dall'Olio]

This is a difficult question, because the answer depends on what you want to show.

The ENCODE researchers faced similar problems, when they had to find a way to visualize expression levels from a lot of tissues. One solution they have found is the ENCODE-RNA-dashboard:

This basically is not much different from an heatmap, but it is interactive, so you can click and get more details about a specific tissue.

Another solution, as suggested bu Suhkdeep, is to use faceting. This is a reproducible example of how to use faceting to generate multiple plots:

> library(reshape)
> d = data.frame("B1"=rnorm(8),"B2"=rnorm(8), "B3"=rnorm(8), "B4"=rnorm(8), "B5"=rnorm(8), "B6"=rnorm(8), "B7"=rnorm(8), "B8"=rnorm(8))
> d

          B1           B2          B3         B4          B5         B6
1 -0.6581045 -1.093919442  0.94578457 -0.1805976  0.41888201 -0.7794898
2 -1.1092189 -0.091769948  0.09502878 -1.4822778 -0.04307963 -0.5021063
3  0.8569934 -0.388095230 -1.06364075  0.2441476 -0.23060652 -1.4263023
4 -0.9435040 -0.791272225 -1.20657936  0.6161711  1.18477321 -0.3969317
5  0.1589559 -0.007835382  0.66982203  0.3872096 -0.88920083 -0.2209863
6  1.4952576  0.549350763 -0.61693139 -1.5470285  0.21826829 -0.7205813
7 -1.5454067 -0.785411708  0.48277576 -1.8998326  0.78415025 -0.8832751
8  1.0721951  0.490277322  1.17584947  0.1968467  1.74636297  1.8247020
          B7         B8
1 -1.7490352 -0.3638126
2  1.1485487  0.7564457
3  0.9900087 -1.1589263
4 -1.2926119  1.4203860
5  3.4772243  0.8022015
6  0.5892454  0.3348479
7 -0.4157224  0.6205421
8 -0.6170603  1.5733568

> d$id = row.names(d)
> d.long = melt.data.frame(d, id.var='id')

# facets with ggplot2

> library(ggplot2)
> qplot(as.integer(id), value, facets=~variable, data=d.long, geom='line')

# facets with lattice

> library(lattice)
> xyplot(value~id2|variable, d.long, type=c('l','p'), layout=c(3,3)) # note: with the layout option you can split the plot into multiple page. This is actually not easy to do in ggplot2.

Answer 2

[Pavel Senin]

This sort of very simple, yet efficient way to obtain plot similar to yours at once, you will need to add proper breaks and axis labels

require(ggplot2)
require(reshape)

# make data matrix 10x100, step 5 for each next series
data = data.frame(  
  matrix(rnorm(1000)+rep(seq(1,50,5),100), nrow=10, byrow=F))

# numeric variables
colnames(data) = paste(seq(1:100))

# attach series names and do the melt
data = cbind(series=factor(seq(1:10), levels=seq(1:10), 
              labels=paste("series_",seq(1:10),sep="")), data)
dm = melt(data)

# plot
(p = ggplot(dm, aes(x=variable, y=value, group=series, colour=series)) +
   geom_line() + theme_bw() + ggtitle("A rough figure of it...") +
   scale_y_continuous("Blocks",breaks=seq(1,50,5), labels=paste("block_",seq(1:10),sep="")) +
   scale_x_discrete("T-s",breaks=seq(1,100,10), labels=paste("T",seq(1:10),sep="")))

[Giovanni M Dall'Olio]

nice idea, you should add a screenshot of the plot to this discussion.

[Pavel Senin]

Alright. Sample added.