Hello everyone,
Currently I am trying to do K - mean clustering on microarray dataset which consists of 127 columns and 1000 rows. When I plot the graph, it gives an error like "figure margins too large". Then, I write this in R console:
par("mar") #It will give current dimensions
par(mar=c(1,1,1,1) #Tried to update the dimensions
But; it did not work. So, can anyone suggest me another way of fixing this problem? (Attached the some part of code in below)
Thanks,
Hasan
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x = as.data.frame(x)
km_out = kmeans(x, 2, nstart = 20)
km_out$cluster
plot(x, col=(km.out$cluster+1), main="K - Means Clustering Results with K=2",xlab"", ylab"", pch=20, cex=2)
>Error in plot.new() : figure margins too large
If x is a data.frame, plot(x) will produce a pairs plot. If x has n columns, a matrix of n x n plots will be drawn. If n is too large, the individual ploty will bee too small (smaller than the space needed already for the margins).
Check how many columns there are in x and if you really want a pairs plot. You may consider a heatmap, using RowSideColors indicating the cluster membership.
Thank you for your response, @DrJochen. I will try your suggestion and hope it will fix the problem.
Hi @Valentin, thank you for your interest. I already tried to move the borders of RStudio but it did not fix the problem, but I will try your second recommendation.
I agree with @Valentin, try
pdf('myplot.pdf')
plot(x, col=(km.out$cluster+1), main="K - Means Clustering Results with K=2",xlab"", ylab"", pch=20, cex=2)
dev.off()
this will produce a pdf file (you can also do the same with .eps format) in the directory.
Hi Hasan, another suggestion, following @valentin and @Flavio. When you are plotting such big plots it may happen that just saving it as a pdf with default width and height parameters will produce a heatmap that has superpositions or some parts can be cut off. If you cannot modify the plot features sizes at least what you can do is customize the pdf size to be able to plot big plots and see all the features in them.
> pdf('name.pdf',width = 8.267, height = 11.692)
Best,
Mar
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