[R] Matrix heatmap

Petr PIKAL petr.pikal at precheza.cz
Thu May 10 18:19:20 CEST 2012


Hi

what is wrong with

 heatmap(as.matrix(test), col=my.colors(25))

with test from your dput

Regards
Petr

> The heat map generated the correct result:
> 
> library(gplots)
> arq <-read.table("l")
> matrix_l <-data.matrix(arq)
> my.colors <-
> colorRampPalette(c
> 
("gray0","gray10","gray20","gray30","gray40","gray50","gray60","gray80","gray90","gray100"))
> heatmap.2(matrix_l,dendrogram="none", Rowv=NA, Colv=NA, 
col=my.colors(256)) 
> 
> --------------------------
> 
> Now I have the following file with 5 data, similar to the above:
> 
>    RF00002   RF00013   RF00100   RF00381   RF00434   RF00453   RF00165 
> RF00496   RF00497
> RF00014   RF00048   RF00234   RF00163   RF00008   RF00094   RF00032 
> RF00028   RF00216
> RF00487   RF00209   RF00465   RF00485   RF00363   RF00366
> RF00002   63   7   5   7   17   12   14   5   23   3   56   14   72   84 
 
> 15   64   20   0   1   8   6   65   3   4
> RF00013   45   7   4   6   17   12   14   5   23   3   56   12   60   84 
 
> 15   64   20   0   0   2   2   65   3   4
> RF00100   22   1   5   3   2   9   0   0   0   0   5   0   16   8   1 0 
> 0   0   0   0   0   26   2   3
> RF00381   63   7   5   13   17   11   3   5   18   3   56   14   33   12 
 
> 2   15   4   18   12   25   11   69   3   4
> RF00434   2   0   0   3   17   11   14   5   23   3   55   12   59   84  

> 15   64   20   0   0   0   0   40   1   3
> RF00453   3   1   0   2   16   12   13   3   7   0   45   12   42   78 
> 15   53   20   0   0   0   0   33   2   0
> RF00165   0   0   0   2   10   1   14   1   7   0   44   12   38   68 13
> 48   20   0   0   0   0   18   0   0
> RF00496   0   0   0   0   0   0   1   5   6   0   0   0   4   2   0   0  

> 0   0   0   0   0   0   0   0
> RF00497   0   0   0   3   10   0   12   5   23   3   40   8   37   77 15
> 64   20   0   0   0   0   20   0   0
> RF00014   0   0   0   0   0   0   0   0   8   3   6   0   0   0   0   0  

> 0   0   0   0   0   0   0   0
> RF00048   3   1   0   3   17   10   14   5   23   3   56   12   59   83  

> 15   64   20   0   0   0   0   52   3   3
> RF00234   62   7   5   6   17   12   14   5   23   3   56   14   70   84 
 
> 15   64   20   0   0   0   1   65   3   4
> RF00163   63   7   5   7   17   12   14   5   23   3   56   14   75   84 
 
> 15   64   21   6   1   10   9   65   3   4
> RF00008   3   1   0   3   17   12   14   5   23   3   56   12   58   84  

> 15   64   20   0   0   0   0   52   3   2
> RF00094   0   0   0   0   0   1   11   0   1   0   0   0   34   73   15  

> 49   20   0   0   0   0   12   0   0
> RF00032   0   0   0   3   10   1   14   5   23   3   56   12   43   80 
> 15   64   20   0   0   0   0   21   0   0
> RF00028   63   7   5   13   17   12   14   5   23   3   56   14   75 84 
> 15   64   30   23   14   25   20   85   3   4
> RF00216   63   7   5   13   17   12   14   5   23   3   56   14   75 84 
> 15   64   28   23   14   25   20   85   3   4
> RF00487   63   7   5   13   17   12   14   5   23   3   56   14   75 84 
> 15   64   28   20   14   25   16   83   3   4
> RF00209   50   7   5   3   2   2   0   0   0   0   1   2   26   4   0 0 
> 1   0   8   25   5   28   3   3
> RF00465   59   7   5   10   7   11   0   0   10   3   11   2   32   9 1 
> 3   6   15   5   14   20   63   3   4
> RF00485   63   7   5   13   17   12   14   5   23   3   56   14   75 84 
> 15   64   26   17   14   25   19   85   3   4
> RF00363   5   3   0   3   10   1   1   5   20   3   50   12   44   24 5 
> 5   0   0   0   0   0   42   3   3
> RF00366   8   2   1   4   14   9   13   5   23   3   52   12   51   68 
> 12   8   0   0   0   0   0   48   3   4
> 
> Now I have the following file with 5 data, similar to the above:
> Is represented by an array of 25x25 and 10x10 not like the previous
> 
> when I give the command dput (arch) it returns me the following output:
> 
> structure(list(RF00002 = c(63L, 45L, 22L, 63L, 2L, 3L, 0L, 0L, 
> 0L, 0L, 3L, 62L, 63L, 3L, 0L, 0L, 63L, 63L, 63L, 50L, 59L, 63L, 
> 5L, 8L), RF00013 = c(7L, 7L, 1L, 7L, 0L, 1L, 0L, 0L, 0L, 0L, 
> 1L, 7L, 7L, 1L, 0L, 0L, 7L, 7L, 7L, 7L, 7L, 7L, 3L, 2L), RF00100 = c(5L, 

> 4L, 5L, 5L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 5L, 5L, 0L, 0L, 0L, 5L, 
> 5L, 5L, 5L, 5L, 5L, 0L, 1L), RF00381 = c(7L, 6L, 3L, 13L, 3L, 
> 2L, 2L, 0L, 3L, 0L, 3L, 6L, 7L, 3L, 0L, 3L, 13L, 13L, 13L, 3L, 
> 10L, 13L, 3L, 4L), RF00434 = c(17L, 17L, 2L, 17L, 17L, 16L, 10L, 
> 0L, 10L, 0L, 17L, 17L, 17L, 17L, 0L, 10L, 17L, 17L, 17L, 2L, 
> 7L, 17L, 10L, 14L), RF00453 = c(12L, 12L, 9L, 11L, 11L, 12L, 
> 1L, 0L, 0L, 0L, 10L, 12L, 12L, 12L, 1L, 1L, 12L, 12L, 12L, 2L, 
> 11L, 12L, 1L, 9L), RF00165 = c(14L, 14L, 0L, 3L, 14L, 13L, 14L, 
> 1L, 12L, 0L, 14L, 14L, 14L, 14L, 11L, 14L, 14L, 14L, 14L, 0L, 
> 0L, 14L, 1L, 13L), RF00496 = c(5L, 5L, 0L, 5L, 5L, 3L, 1L, 5L, 
> 5L, 0L, 5L, 5L, 5L, 5L, 0L, 5L, 5L, 5L, 5L, 0L, 0L, 5L, 5L, 5L
> ), RF00497 = c(23L, 23L, 0L, 18L, 23L, 7L, 7L, 6L, 23L, 8L, 23L, 
> 23L, 23L, 23L, 1L, 23L, 23L, 23L, 23L, 0L, 10L, 23L, 20L, 23L
> ), RF00014 = c(3L, 3L, 0L, 3L, 3L, 0L, 0L, 0L, 3L, 3L, 3L, 3L, 
> 3L, 3L, 0L, 3L, 3L, 3L, 3L, 0L, 3L, 3L, 3L, 3L), RF00048 = c(56L, 
> 56L, 5L, 56L, 55L, 45L, 44L, 0L, 40L, 6L, 56L, 56L, 56L, 56L, 
> 0L, 56L, 56L, 56L, 56L, 1L, 11L, 56L, 50L, 52L), RF00234 = c(14L, 
> 12L, 0L, 14L, 12L, 12L, 12L, 0L, 8L, 0L, 12L, 14L, 14L, 12L, 
> 0L, 12L, 14L, 14L, 14L, 2L, 2L, 14L, 12L, 12L), RF00163 = c(72L, 
> 60L, 16L, 33L, 59L, 42L, 38L, 4L, 37L, 0L, 59L, 70L, 75L, 58L, 
> 34L, 43L, 75L, 75L, 75L, 26L, 32L, 75L, 44L, 51L), RF00008 = c(84L, 
> 84L, 8L, 12L, 84L, 78L, 68L, 2L, 77L, 0L, 83L, 84L, 84L, 84L, 
> 73L, 80L, 84L, 84L, 84L, 4L, 9L, 84L, 24L, 68L), RF00094 = c(15L, 
> 15L, 1L, 2L, 15L, 15L, 13L, 0L, 15L, 0L, 15L, 15L, 15L, 15L, 
> 15L, 15L, 15L, 15L, 15L, 0L, 1L, 15L, 5L, 12L), RF00032 = c(64L, 
> 64L, 0L, 15L, 64L, 53L, 48L, 0L, 64L, 0L, 64L, 64L, 64L, 64L, 
> 49L, 64L, 64L, 64L, 64L, 0L, 3L, 64L, 5L, 8L), RF00028 = c(20L, 
> 20L, 0L, 4L, 20L, 20L, 20L, 0L, 20L, 0L, 20L, 20L, 21L, 20L, 
> 20L, 20L, 30L, 28L, 28L, 1L, 6L, 26L, 0L, 0L), RF00216 = c(0L, 
> 0L, 0L, 18L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 6L, 0L, 0L, 0L, 
> 23L, 23L, 20L, 0L, 15L, 17L, 0L, 0L), RF00487 = c(1L, 0L, 0L, 
> 12L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 14L, 14L, 
> 14L, 8L, 5L, 14L, 0L, 0L), RF00209 = c(8L, 2L, 0L, 25L, 0L, 0L, 
> 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L, 0L, 25L, 25L, 25L, 25L, 
> 14L, 25L, 0L, 0L), RF00465 = c(6L, 2L, 0L, 11L, 0L, 0L, 0L, 0L, 
> 0L, 0L, 0L, 1L, 9L, 0L, 0L, 0L, 20L, 20L, 16L, 5L, 20L, 19L, 
> 0L, 0L), RF00485 = c(65L, 65L, 26L, 69L, 40L, 33L, 18L, 0L, 20L, 
> 0L, 52L, 65L, 65L, 52L, 12L, 21L, 85L, 85L, 83L, 28L, 63L, 85L, 
> 42L, 48L), RF00363 = c(3L, 3L, 2L, 3L, 1L, 2L, 0L, 0L, 0L, 0L, 
> 3L, 3L, 3L, 3L, 0L, 0L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), RF00366 = c(4L, 

> 4L, 3L, 4L, 3L, 0L, 0L, 0L, 0L, 0L, 3L, 4L, 4L, 2L, 0L, 0L, 4L, 
> 4L, 4L, 3L, 4L, 4L, 3L, 4L)), .Names = c("RF00002", "RF00013", 
> "RF00100", "RF00381", "RF00434", "RF00453", "RF00165", "RF00496", 
> "RF00497", "RF00014", "RF00048", "RF00234", "RF00163", "RF00008", 
> "RF00094", "RF00032", "RF00028", "RF00216", "RF00487", "RF00209", 
> "RF00465", "RF00485", "RF00363", "RF00366"), class = "data.frame", 
row.names
> = c("RF00002", 
> "RF00013", "RF00100", "RF00381", "RF00434", "RF00453", "RF00165", 
> "RF00496", "RF00497", "RF00014", "RF00048", "RF00234", "RF00163", 
> "RF00008", "RF00094", "RF00032", "RF00028", "RF00216", "RF00487", 
> "RF00209", "RF00465", "RF00485", "RF00363", "RF00366"))
> 
> but he is not in scale with the gray color I wanted, like he looks like
> this:
> 
> http://r.789695.n4.nabble.com/file/n4621356/Captura_de_tela-14.png 
> 
> I  wanted to do, that it generates histogram, stayed the count from 0 to 
25
> (because I have 25 data) and the value of (0-100)
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/Matrix-
> heatmap-tp4619084p4621356.html
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> 
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