[R] Drawing Heatmap using gplots

[khush ........]

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