Hi,

I am using heatmap.2 of gplots to make heatmaps of my the file. I am giving
my code for the same ..

library(gplots)
        x=read.table("1.txt", header=TRUE)
mat=data.matrix(x)

        heatmap.2(mat, col=greenred(75),
Rowv=TRUE,
Colv=TRUE,
distfun = dist,
hclustfun = hclust,
dendrogram = c("both"),
scale = c("row"),
na.rm=TRUE,
trace="none",
sepwidth=c(0.05,0.05),
margins = c(5, 10),
xlab = "EXPRESSIONS", ylab = "GENES",
labRow = NULL,
labCol = NULL,
key=TRUE,
keysize=1,
density.info=c("none"),
)

my file is like this ...

        CAF     CAS     INF     INS     AP1     AP3     AGM     SAP
S04     S52     LEF     LES     ROF     ROS     GSE     SIF     SIS
At1g01940       107     111     20      27      40      52      27
8       6       24      40      18      67      85      35      56      118
At1g26940       35      27      30      28      15      41      12
73      6       15      21      11      60      35      6       24      77
At1g53720       34      35      16      52      15      27      24
13      3       12      35      6       43      51      1       21      25
At1g53780       2       6       2       11      6       9       7
0       0       0       6       10      5       19      0       0       0
At1g74070       0       16      18      41      18      23      13
9       68      7       41      39      0       6       29      66      53
At2g15790       0       61      0       2       1       1       2
0       0       5       0       0       0       8       0       0       47
At2g16600       703     1157    414     299     616     1235    1208
645     2574    3308    473     183     1797    1156    455     735     596
At2g21130       240     154     270     615     78      265     1257
769     704     126     16      22      70      1       20      140     208
At2g29960       81      145     23      45      62      37      49
25      52      39      48      27      31      151     0       35      293
At2g36130       248     36      88      46      32      110     86
58      10      6       278     34      252     96      0       190     84
At2g38730       26      8       16      6       4       18      0
0       0       0       0       0       6       1       0       22      0
At2g47320       105     82      87      88      42      91      118
158     84      96      87      132     394     301     30      378     302
At3g01480       0       6       174     48      36      159     52
79      56      101     0       88      8       2       103     207     41
At3g15520       0       0       86      70      30      52      17
19      47      7       70      43      68      0       33      38      45
At3g22920       0       0       0       0       0       0       0
0       0       0       0       0       0       0       0       0       0
At3g44600       62      166     62      48      24      39      26
14      0       4       56      32      106     155     2       28      18


I have certain queries regarding the same.


1. why the heat map is totally different from what the sequence of
information is?
2. Is there any way to arrange the data based on the expression pattern of
the genes or some other way, which make some sense out of data.
3. I have some color issues as the number of genes increases the green and
black colors are not as much as prominent as red?

Thank you so much for your help in advance.

Thank you
Khushwant

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