I received an error in heatmap.2, and I found similar error here R : knnImputation Giving Error but it doesn't have an answer yet. I couldn't understand the problem. I am new to this world, sorry in advance if there is any mistake.
I have a dataframe df with 144 rows,177 columns which shows the monthly averages of years between 2005-2016 by timeAverage function openair package.
Here the small example from df:
date Year Month Adana-Catalan Adana-Dogankent Adana-Meteoroloji
2008/09/01 2008 9 NaN NaN NaN
2008/10/01 2008 10 NaN NaN 1.7948718
2008/11/01 2008 11 NaN NaN 2.0909091
2008/12/01 2008 12 1.2694064 12.2384106 0.7272727
2009/01/01 2009 1 2.3150358 12.7479339 10.3779762
2009/02/01 2009 2 2.8241107 18.4320175 2.4494949
2009/03/01 2009 3 2.0401606 8.4597523 1.6529412
2009/04/01 2009 4 1.8604651 4.8560000 1.1267606
2009/05/01 2009 5 2.1087719 1.8202247 NaN
2009/06/01 2009 6 4.0695103 2.1463415 1.1111111
2009/07/01 2009 7 5.4016393 8.1298905 NaN
2009/08/01 2009 8 0.1313869 16.9874411 NaN
2009/09/01 2009 9 NaN 5.3753943 NaN
2009/10/01 2009 10 1.6626506 8.8000000 1.8388889
2009/11/01 2009 11 1.4177632 NaN 3.9879154
2009/12/01 2009 12 0.9644128 NaN 5.0281457
2010/01/01 2010 1 0.2608696 4.0898876 3.1981424
2010/02/01 2010 2 0.7619048 NaN 4.3169811
remove non-numeric columns:
df.monthly <- df[,-c(1:3)] #remove non-numeric columns
df.monthly.un <- unlist(df.monthly) #unlist the list
df.monthly.un[is.nan(df.monthly.un)] <- -999 #replace NaNs with -999
monthly.dim <- dim(df.monthly)
monthly.frame <- matrix(df.monthly.un, monthly.dim) #convert unlist to matrix
then I calculated distance matrix and produced dendograms. Finally, I used heatmap.2 to produce heatmap with dendograms.
monthly.dist <- dist(monthly.frame)
monthly.hclust <- hclust(monthly.dist, method="complete")
monthly.dist2 <- dist(t(monthly.frame))
colClust <- as.dendrogram(hclust(monthly.dist2, method="complete"))
rowClust <- as.dendrogram(monthly.hclust)
colpalette <- colorRampPalette(c("red","blue","green"))(n=100)
heatmap.2(monthly.frame, scale="none",
col=colpalette, trace= "none", cexRow=0.6, cexCol=1,
cex.main=0.7, key=T, Rowv=rowClust, labRow=df[,1],
main=expression("2005-2016 SO"[2] * " (ug/m"^3*")"))
However, when I run the code, it gives the error:
Error: Column indexes must be at most 1 if positive, not 22, 23, 24, 25, 21, 18, 19, 20, 16, 17, 12, 10, 11, 15, 13, 14, 3, 9, 8, 4, 7, 5, 6, 2, 124, 125, 121, 122, 123, 133, 132, 131, 134, 135, 126, 129, 127, 128, 130, 136, 137, 143, 144, 141, 142, 138, 139, 140, 57, 58, 55, 56, 42, 47, 41, 40, 36, 38, 37, 39, 46, 43, 44, 45, 34, 35, 26, 27, 28, 29, 30, 31, 32, 33, 59, 54, 53, 48, 49, 50, 51, 112, 116, 117, 114, 115, 88, 89, 52, 60, 63, 70, 75, 73, 74, 79, 77, 76, 78, 66, 67, 62, 65, 71, 64, 61, 72, 97, 87, 85, 86, 90, 98, 91, 83, 84, 92, 94, 96, 93, 95, 68, 69, 82, 80, 81, 113, 110, 111, 109, 118, 119, 120, 101, 105, 103, 104, 99, 106, 100, 102, 107, 108
Any idea why this error occurs? Thanks in advance!