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I was reading through this blog post on R-bloggers and I'm confused by the last section of the code and can't figure it out.

http://www.r-bloggers.com/self-organising-maps-for-customer-segmentation-using-r/

I've attempted to recreate this with my own data. I have 5 variables that follow an exponential distribution with 2755 points.

I am fine with and can plot the map that it generates:

plot(som_model, type="codes")

enter image description here

The section of the code I don't understand is the:

var <- 1
var_unscaled <- aggregate(as.numeric(training[,var]),by=list(som_model$unit.classif),FUN = mean, simplify=TRUE)[,2]
plot(som_model, type = "property", property=var_unscaled, main = names(training)[var], palette.name=coolBlueHotRed)

As I understand it, this section of the code is suppose to be plotting one of the variables over the map to see what it looks like but this is where I run into problems. When I run this section of the code I get the warning:

Warning message:
In bgcolors[!is.na(showcolors)] <- bgcol[showcolors[!is.na(showcolors)]] :
number of items to replace is not a multiple of replacement length

and it produces the plot:

enter image description here

Which just some how doesn't look right...

Now what I think it has come down to is the way the aggregate function has re-ordered the data. The length of var_unscaled is 789 and the length of som_model$data, training[,var] and unit.classif are all of length 2755. I tried plotting the aggregated data, the result was no warning but an unintelligible graph (as expected).

Now I think it has done this because unit.classif has a lot of repeated numbers inside it and that's why it has reduced in size.

The question is, do I worry about the warning? Is it producing an accurate graph? What exactly is the "Property"'s section looking for in the plot command? Is there a different way I could "Aggregate" the data?

James Willcox
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  • If the plot if not correct then yes, worry about the warning. In reality, you should always be concerned with why you are getting a warning. I haven't fully checked it out, but I noticed you have a subset on the end of `aggregate`. Is that necessary? – Rich Scriven Sep 22 '14 at 01:19
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    You should provide a [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) so we can run the same code as you and get the same error. Otherwise we really have no way of knowing how your data is stored in each of those objects or how they should be combined in the plot statement. – MrFlick Sep 22 '14 at 03:00
  • Where does the palette `coolBlueHotRed` come from, and what is its length? It may well be configured to match the example data, not your data. – Carl Witthoft Sep 22 '14 at 11:37
  • the coolBlueHotRed pallet is: coolBlueHotRed <- function(n, alpha = 1) { rainbow(n, end=4/6, alpha=alpha)[n:1] } But I can assure you the colour pallet is not the issue because I've tried the code without it and it had the same error. As for the data I'm sorry but I can't provide it as it is confidential but If you give me a moment Ill try and fit a distribution to it so we can create some similar data – James Willcox Sep 22 '14 at 22:33

3 Answers3

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I think that you have to create the palette color. If you put the argument 

coolBlueHotRed <- function(n, alpha = 1) {rainbow(n, end=4/6, alpha=alpha)[n:1]}

and then try to get a plot, for example

plot(som_model, type = "count", palette.name = coolBlueHotRed)

the end is succesful.

This link can help you: http://rgm3.lab.nig.ac.jp/RGM/R_rdfile?f=kohonen/man/plot.kohonen.Rd&d=R_CC

cryo111
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user5250517
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1

I think that not all of the cells on your map have points inside. You have 30 by 30 map and about 2700 points. In average it's about 3 points per cell. With high probability some cells have more than 3 points and some cells are empty.

The code in the post on R-bloggers works well when all of the cells have points inside.

To make it work on your data try change this part: 

var <- 1
var_unscaled <- aggregate(as.numeric(training[, var]), by = list(som_model$unit.classif), FUN = mean, simplify = TRUE)[, 2]
plot(som_model, type = "property", property = var_unscaled, main = names(training)[var], palette.name = coolBlueHotRed)

with this one:

var <- 1
var_unscaled <- aggregate(as.numeric(data.temp[, data.classes][, var]), 
                          by = list(som_model$unit.classif), 
                          FUN = mean, 
                          simplify = T)
v_u <- rep(0, max(var_unscaled$Group.1))
v_u[var_unscaled$Group.1] <- var_unscaled$x
plot(som_model, 
     type = "property", 
     property = v_u, 
     main = colnames(data.temp[, data.classes])[var], 
     palette.name = coolBlueHotRed)

Hope it helps.

Dreamastiy
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  • I agree. If any of your cells are empty that is why your code doesn't work. I have the exact same problem – pmanDS Jun 05 '21 at 21:19
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Just add these functions to your script: 

coolBlueHotRed <- function(n, alpha = 1) {rainbow(n, end=4/6, alpha=alpha)[n:1]}

pretty_palette <- c("#1f77b4","#ff7f0e","#2ca02c", "#d62728","#9467bd","#8c564b","#e377c2")
Sahil Mittal
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Shiladitya Biswas
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