Class07 Answer:

Use R to create a simple heatmap

After some time with Google, I did this lab.

The script looks like this:


# hm10.r

# Ref:
# https://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/

# Demo:
# R -f hm10.r

# I should load nba data:
#nba = read.csv("http://datasets.flowingdata.com/ppg2008.csv", sep=",")
nba = read.csv("ppg2008.csv", sep=",")
# I should order by PTS column:
nba = nba[order(nba$PTS),]

# I should identify each row by Name instead of an integer:
row.names(nba) = nba$Name

# I should remove the Name column which is the first column:
nba = nba[,2:20]

# I should convert nba to a matrix:
nba_x = data.matrix(nba)

png('hm10.png',width=800, units='px', pointsize=22, height=1100)

heatmap(nba_x, Rowv=NA, Colv=NA, scale="column")

dev.off()

I saw this:


dan@e80:~/ml4us/public/class07 $ 
dan@e80:~/ml4us/public/class07 $ 
dan@e80:~/ml4us/public/class07 $ R -f hm10.r

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # hm10.r
> 
> # Ref:
> # https://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/
> 
> # Demo:
> # R -f hm10.r
> 
> # I should load nba data:
> #nba = read.csv("http://datasets.flowingdata.com/ppg2008.csv", sep=",")
> nba = read.csv("ppg2008.csv", sep=",")
> # I should order by PTS column:
> nba = nba[order(nba$PTS),]
> 
> # I should identify each row by Name instead of an integer:
> row.names(nba) = nba$Name
> 
> # I should remove the Name column which is the first column:
> nba = nba[,2:20]
> 
> # I should convert nba to a matrix:
> nba_x = data.matrix(nba)
> 
> png('hm10.png',width=800, units='px', pointsize=22, height=1100)
> 
> heatmap(nba_x, Rowv=NA, Colv=NA, scale="column")
> 
> dev.off()
null device 
          1 
> 
dan@e80:~/ml4us/public/class07 $ 
dan@e80:~/ml4us/public/class07 $ 
dan@e80:~/ml4us/public/class07 $ 

The heatmap looks like this:

Class07 Lab


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