Hi,
I am using heatmap.2 of gplots to make heatmaps of my the attached 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"),
)
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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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
At3g55920 42 52 27 6 11 28 25 68 82 10 15 33 27 17 1 24 81
At3g56070 234 136 112 136 112 260 128 150 0 24 106 18 322 222 20 70 88
At3g62030 34 109 241 129 181 338 304 595 463 849 810 406 18 94 399 566 1992
At3g63400 138 138 144 60 63 57 60 26 53 32 82 66 143 127 91 87 37
At3g66654 79 45 37 15 16 16 23 17 0 59 88 25 40 65 12 50 23
At4g17070 39 103 4 18 33 19 22 33 15 81 56 28 7 100 32 7 41
At4g32420 71 112 59 125 81 103 108 93 30 11 69 30 17 80 7 24 93
At4g33060 164 106 70 20 23 42 23 9 0 14 39 47 74 92 14 222 252
At4g34870 2990 16 3272 320 421 433 311 434 104 19 1532 97 6519 312 345 3160 75
At4g34960 101 38 300 1 1 7 2 0 0 0 33 0 172 14 0 118 52
At4g38740 5034 2272 1986 908 513 692 927 708 116 244 1548 306 3198 1340 91 1012
459
At5g13120 44 0 170 12 24 23 0 50 4 4 236 6 166 0 4 238 0
At5g35100 33 15 197 65 51 57 44 68 82 76 106 79 24 7 2 266 21
At5g58710 464 366 234 365 243 280 218 500 78 260 324 178 548 411 32 918 580
At5g67530 25 36 37 42 38 25 52 124 0 1 11 23 20 83 0 8 12
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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