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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