I'm new to R and using gplots package to generate a heat map for a list of 52 proteins. But the output image does not contain the entire list of proteins (displays only 26) on the right. The image is hazy too. I would be thankful if someone can help me with this. This is the generated heat map.
Below is the script:
library(gplots)
library(RColorBrewer)
library(colorspace)
mat_val <- read.csv("HM5.txt", sep="\t", header = T, row.names=1)
data.m <- as.matrix(mat_val)
data.m
normalization<-function(x){
dimm=dim(x)
for(i in 1:dimm[1]){
m <- mean(x[i,], na.rm=TRUE)
s <- sd(x[i,],na.rm=TRUE)
x[i,]=(x[i,]-m)/s
}
return(x)
}
data.m1<-normalization(data.m)
png("plot.png")
heatmap.2( data.m1,
col = colorpanel(100,"red","yellow","green"),
#margins = c(12, 22),
trace = "none",
xlab = "Comparison",
#lhei = c(2, 8),
scale = c("none"),
symbreaks = min(data.m1, na.rm=TRUE),
na.color="grey",
cexRow = 0.5, cexCol = 0.7,
main = "DE genes",
dendrogram = "both",
Colv = TRUE )
dev.off()
Below is the data set HM5.txt
HM5 <- structure( list( LM1 = c( 0.8937, 0.9836, 0.9459, 1.1011, 1.0467, 0.9041, 1.0674, 0.9432, 1.1349, 0.9217, 1.0271, 0.6252, 0.7526, 0.7709, 0.7071, 1.2038, 1.0878, 0.868, 0.968, 0.9982, 1.0122, 0.9584, 0.6044, 0.5609, 0.7869, 0.7216, 1.2259, 1.3198, 0.8333, 1.0721, 1.1986, 0.8265, 1.0643, 0.9962, 1.1233, 1.0151, 0.6536, 0.7409, 1.4568, 1.5307, 2.0551, 1.1301, 0.9372, 0.8736, 0.5929, 0.7746, 0.6439, 1.203, 1.4402, 2.6744, 2.3252, 1.8372 ), LM2 = c( 1.0823, 1.0825, 1.0894, 1.1223, 1.1964, 1.1082, 1.0156, 1.0506, 1.0878, 1.1048, 1.0565, 1.1332, 1.1088, 1.0501, 0.9579, 1.0227, 1.2164, 0.752, 1.2088, 1.2981, 0.6642, 1.2335, 1.4094, 1.2932, 1.2304, 1.3789, 0.7759, 1.2251, 1.1078, 1.0707, 1.0467, 1.0525, 1.1391, 0.9921, 0.9808, 0.9604, 0.9007, 0.9912, 1.0403, 1.1358, 0.8401, 1.2952, 1.2235, 1.4171, 1.4848, 1.6692, 1.3173, 1.2998, 1.2054, 1.4887, 1.8244, 1.6395 ), LM3 = c( 1.092, 1.016, 0.8963, 1.1557, 1.105, 1.0601, 1.0887, 1.1252, 1.1524, 0.8704, 1.0604, 1.0055, 0.9946, 0.9759, 0.9538, 1.0552, 1.0429, 1.0994, 1.0292, 1.125, 1.1291, 1.0088, 0.9754, 0.903, 1.0734, 0.9716, 0.876, 1.182, 1.3055, 1.2712, 1.3415, 1.2576, 1.418, 1.2013, 1.3783, 1.3101, 0.6731, 0.7606, 1.2782, 1.266, 0.7436, 1.2185, 1.2036, 1.2982, 0.6701, 1.4568, 1.2284, 1.2022, 1.2899, 1.96, 2.297, 1.6332 ), LF1 = c( 0.1974, 0.1606, 0.1804, 0.249, 0.2121, 0.2153, 0.2076, 0.1876, 0.2273, 0.255, 0.2059, 0.2699, 0.1814, 0.179, 0.1812, 0.1993, 0.2228, 0.1719, 0.2003, 0.1839, 0.1951, 0.1965, 0.2059, 0.2082, 0.1972, 0.2323, 0.2332, 0.1848, 0.1924, 0.1767, 0.1998, 0.2073, 0.1545, 0.201, 0.276, 0.1984, 0.1714, 0.172, 0.2031, 0.2144, 0.2137, 0.1908, 0.2024, 0.159, 0.1744, 0.2559, 0.1826, 0.1736, 0.1829, 0.2756, 0.4066, 0.2312 ), LF2 = c( 1.7865, 1.0568, 0.8017, 0.492, 3.1333, 0.9376, 1.4454, 0.7178, 0.3192, 0, 1.3183, 0.3565, 0.9817, 0.4093, 0.2014, 1.1169, 0.3251, 0.929, 0.1644, 1.0186, 0.863, 3.3729, 0.9638, 0.9462, 3.1623, 0.879, 3.4041, 1.2942, 0.9638, 0.227, 0.4246, 1, 0.1614, 0.4018, 3.342, 0.7943, 1.0093, 0.8241, 1.6144, 2.1086, 4.4875, 0.9638, 1.9055, 0.3631, 0.9376, 1.4322, 0.8872, 1.0375, 0.6368, 1.1912, 10.7647, 2.3768 ), MM1 = c( 0.831, 0.8069, 0.7695, 0.7954, 0.7055, 0.843, 0.7051, 0.7632, 0.8037, 0.6859, 1.0166, 0.5746, 0.7053, 0.7693, 0.677, 0.7576, 0.8744, 0.6963, 0.8302, 0.809, 0.9399, 0.9138, 0.7768, 0.7281, 0.9617, 0.9705, 0.9237, 1.0768, 0.8918, 0.7429, 0.8888, 0.8283, 0.7535, 0.7858, 0.7991, 0.6786, 0.9591, 0.9289, 0.8007, 0.8251, 1.1534, 0.8977, 1.0682, 1.0365, 0.7455, 0.9681, 0.6652, 1.186, 0.8393, 1.6303, 1.5202, 1.8395 ), MM2 = c( 0.5761, 0.4992, 0.5918, 0.5114, 0.5053, 0.4851, 0.6461, 0.6314, 0.5643, 0.3787, 0.4688, 0.491, 0.5192, 0.5749, 0.6055, 0.6132, 0.5116, 0.499, 0.4811, 0.6668, 0.7295, 0.5376, 0.3647, 0.3375, 0.506, 0.5035, 0.4228, 0.5301, 0.6051, 0.6267, 0.6035, 0.6088, 0.7325, 0.4821, 0.6447, 0.5985, 0.3752, 0.367, 0.357, 0.6541, 0.303, 0.5317, 0.6313, 0.4456, 0.3614, 0.3772, 0.5478, 0.5865, 0.5677, 0.7236, 1.0412, 0.5946 ), MF1 = c( 1.1244, 1.1473, 1.1559, 1.0325, 1.2822, 1.1218, 1.436, 1.147, 1.087, 1.0142, 1.4559, 1.2502, 1.1184, 1.0561, 0.9864, 1.1173, 1.1226, 1.2358, 1.1484, 1.0245, 1.223, 1.203, 1.3244, 1.2962, 1.1965, 1.0276, 1.6954, 1.3128, 1.1993, 1.3661, 1.2898, 1.2275, 1.3777, 1.1025, 1.1791, 1.0395, 0.9376, 1.1278, 1.3988, 1.1576, 1.2929, 1.1729, 1.0881, 1.2311, 1.2313, 1.064, 1.1903, 1.3236, 1.0529, 1.2801, 1.2666, 1.5624 ), MF2 = c( 1.4588, 0.9817, 0.2858, 3.1333, 0.5058, 1.0186, 0.8166, 0.8017, 1.2134, 0, 0.929, 1.0765, 0.5012, 0.3945, 0.5346, 0.9036, 0.5248, 1, 1.888, 0.8551, 2.208, 5.0582, 0.9727, 0.955, 2.6546, 0.8472, 4.529, 0.2168, 0.9817, 0.6982, 0.863, 2.8054, 0.6138, 0.1343, 0.5346, 1.0186, 0.9817, 0.6252, 0.9204, 1.6749, 9.8175, 0.9908, 1.5276, 1.5849, 0.9376, 1.4723, 0.9376, 0.929, 4.529, 1, 0.2249, 0.3908 ), HMF = c( 0.6306, 0.6591, 0.5978, 1.1586, 0.6905, 0.642, 0.7358, 0.6064, 1.1143, 0.81, 0.5564, 0.7242, 0.8195, 0.6615, 0.4918, 0.7781, 0.7858, 0.6167, 0.6311, 0.885, 0.6726, 0.732, 0.5722, 0.606, 0.7687, 0.7518, 1.8878, 0.9485, 0.6481, 0.8183, 0.751, 0.8144, 0.7969, 0.7051, 0.7223, 0.8483, 0.7188, 0.4508, 1.0244, 0.873, 1.3346, 0.7926, 0.6934, 0.4721, 0.6227, 0.7871, 0.5684, 0.9085, 0.7436, 0.9759, 1.2711, 0.8888 ), HM1 = c( 1.2571, 1.3125, 1.1627, 1.4683, 1.5069, 1.4465, 1.7694, 1.2702, 1.4702, 1.2355, 1.4315, 0.9321, 0.9661, 1.1486, 1.1179, 1.5893, 1.4764, 1.2092, 1.4771, 1.3616, 0.9069, 1.3953, 1.1422, 1.0394, 1.3766, 1.161, 2.5024, 2.0681, 1.1532, 1.5672, 1.6332, 1.3973, 1.7254, 1.2994, 1.7251, 1.3708, 0.8927, 1.2513, 1.8322, 1.7957, 1.3296, 1.7005, 1.532, 1.2533, 1.3126, 1.5664, 0.9914, 1.5967, 2.1548, 2.9774, 3.2983, 2.6167 ), HM2 = c( 1.7311, 1.621, 1.5349, 1.555, 1.5374, 1.423, 1.2358, 1.4572, 1.5495, 1.3658, 1.3666, 1.5235, 1.6188, 1.4307, 1.2981, 1.49, 1.7852, 1.1065, 1.5073, 1.4628, 1.3851, 1.8537, 1.8606, 1.769, 1.6717, 1.8653, 1.5592, 2.2977, 1.6822, 1.6933, 1.7937, 1.69, 2.099, 1.5253, 1.3896, 1.4641, 1.4912, 1.5688, 1.4747, 1.588, 1.7314, 1.7555, 1.7408, 1.804, 1.8974, 1.7766, 1.7087, 1.8565, 1.4012, 1.53, 1.4294, 2.3486 ), HM3 = c( 1.2614, 1.0042, 1.0615, 1.0201, 1.0339, 1.3403, 1.1221, 1.1823, 1.1311, 0.7721, 1.2186, 0.9017, 0.769, 1.0421, 0.9936, 0.9306, 1.0012, 1.0606, 1.2946, 0.9714, 1.3916, 1.0472, 1.0822, 0.9817, 1.0255, 1.0481, 0.766, 1.053, 1.2499, 1.1712, 1.3263, 1.1321, 1.6186, 1.2289, 1.1356, 1.2055, 0.6229, 1.0405, 1.225, 1.1021, 0.9535, 1.217, 1.1489, 1.3058, 0.5363, 0.4941, 1.1499, 1.0487, 1.3848, 2.2277, 3.279, 1.7359 ), HF1 = c( 0.8302, 0.6699, 0.695, 0.7853, 0.9915, 1.2059, 0.8226, 0.7975, 0.7809, 0.6842, 1.0005, 0.9192, 0.7052, 0.6844, 0.6063, 0.7681, 0.7405, 0.7842, 1.0554, 0.7723, 0.7354, 0.8431, 1.9057, 1.8485, 0.8374, 0.7467, 0.941, 0.898, 0.7842, 0.8711, 0.8316, 0.8792, 0.7465, 0.7058, 0.8746, 0.6663, 0.5641, 0.7089, 0.7961, 0.728, 0.9857, 0.7191, 0.8145, 0.7518, 1.3629, 0.7532, 0.7998, 0.9709, 0.841, 0.7584, 0.9637, 1.0729 ), HF2 = c( 0.5445, 0.955, 1.3804, 3.767, 0.6081, 0.9817, 1.5417, 0.6855, 1.6293, 0, 1.028, 0.5598, 0.5105, 0.2884, 0.4055, 1.2134, 0.227, 0.9817, 1.9231, 0.9908, 0.4207, 11.8032, 0.9908, 0.9727, 13.9316, 3.5645, 1.803, 0.52, 0.929, 0.6138, 1.1695, 0.4966, 0.4831, 0.4246, 0.2014, 0.7798, 0.955, 0.3597, 0.1871, 0.6368, 1.9588, 0.9727, 2.9648, 0.2443, 0.9817, 0.2312, 0.8872, 0.8872, 2.7797, 1.1695, 8.7096, 0.1343 ) ), class = "data.frame", row.names = c( "P01031", "P01008", "P04217", "P07357", "P10909", "P00488", "P27169", "Q96IY4", "P07360", "Q9NZP8", "C9JF17", "P02748", "Q06033", "D6R934", "P02747", "P80108", "B4E1Z4", "P02774", "P05160", "P23142", "P05543", "P02760", "P02675", "P02679", "P25311", "P02745", "P0C0L5", "P06727", "P02790", "P00747", "P00734", "P05546", "P43652", "P22792", "P02649", "P02743", "P01023", "P51884", "G3V2W1", "O95445", "P0C0L4", "P01024", "P36955", "P19652", "P02671", "P13671", "P02763", "P02647", "Q5VY30", "K7ER74", "B0YIW2", "K7ERI9" ) )
Edit 1: Attached a snippet of the dataset HM5.txt
