Axis range when using plot - r

I am trying to create the following plot with the black background.
I have used this commands
x <- c(134.21, 139.12, 145.7, 148.81, 157.27, 128.4, 147.44, 133.72, 147.26, 137.26, 136.93, 137.37, 145.4, 141.74, 145.35, 130.01, 140.1, 136.3, 141.02, 137.5, 139.62, 140.05, 139.55, 135.55, 138.93, 140.07, 154.76, 138, 146.95, 139.62, 137.38, 146.27, 148.23, 152.65, 137.82, 145.28, 135.52, 152.97, 138.03, 138.82, 149.63, 131.83, 132.68, 151.5, 148.5, 142.79, 131.76, 132.83)
y <- c(0.0212, 0.1136, 0.0842, -0.0285, -0.1362, 0.1928, 0.0491, 0.0653, 0.0358, 0.082, -3e-04, 0.0659, -0.1173, -0.0707, -0.1298, 0.2789, 0.0092, 0.1105, -0.0603, 0.0409, 0.021, 0.0479, 0.0495, 0.1562, -0.1276, 0.0486, -0.519, 0.0548, 0.0072, 0.05, -0.0595, -0.0469, -0.1501, -0.2125, -0.0205, 0.0293, 0.0025, 3e-04, 0.0013, 0.0286, -0.1069, 0.1171, 0.1073, -0.0799, 0.0197, -0.0664, -0.0976, 0.0696 )
par(bg="black")
plot(x,y,pch=21,bg="white",col="red",cex=2,lwd=1,col.lab="white",col.axis="white",cex.lab=1,main="Scatterplot",font.main=1)
axis(1,col="white",col.axis="yellow")
axis(2,col="white",col.axis="yellow")
abline(lm(y~x),col="red",lwd=3)
I have two problems that I can not solve:
I can not see the title 'Scatterplot' on the image
It seems that the lines are cropped, when plotting with a white background the x,y axis seem ok. However I need this graph with a dark background.
Does anyone have an idea how to resolve this?


Not sure what you mean about lines being cropped, but maybe this is what you want:
plot(x, y, pch=21, bg="white", col="red", cex=2, lwd=1, col.lab="white",
col.axis="white", cex.lab=1, col.main="white", main="Scatterplot", font.main=1)
axis(1, col="white", col.axis="yellow")
axis(2, col="white", col.axis="yellow")
abline(lm(y ~ x), col="red", lwd=3)
box(col="white", lwd=2)
)


This should do it:
x <- c(134.21, 139.12, 145.7, 148.81, 157.27, 128.4, 147.44, 133.72, 147.26, 137.26, 136.93, 137.37, 145.4, 141.74, 145.35, 130.01, 140.1, 136.3, 141.02, 137.5, 139.62, 140.05, 139.55, 135.55, 138.93, 140.07, 154.76, 138, 146.95, 139.62, 137.38, 146.27, 148.23, 152.65, 137.82, 145.28, 135.52, 152.97, 138.03, 138.82, 149.63, 131.83, 132.68, 151.5, 148.5, 142.79, 131.76, 132.83)
y <- c(0.0212, 0.1136, 0.0842, -0.0285, -0.1362, 0.1928, 0.0491, 0.0653, 0.0358, 0.082, -3e-04, 0.0659, -0.1173, -0.0707, -0.1298, 0.2789, 0.0092, 0.1105, -0.0603, 0.0409, 0.021, 0.0479, 0.0495, 0.1562, -0.1276, 0.0486, -0.519, 0.0548, 0.0072, 0.05, -0.0595, -0.0469, -0.1501, -0.2125, -0.0205, 0.0293, 0.0025, 3e-04, 0.0013, 0.0286, -0.1069, 0.1171, 0.1073, -0.0799, 0.0197, -0.0664, -0.0976, 0.0696 )
par(bg="black")
plot(x,y, xlim = c(125, 160), ylim = c(-0.6, 0.4), pch=21,bg="white",col="red",cex=2,lwd=1,col.lab="white",col.axis="white",cex.lab=1, col.main ="white", main="Scatterplot",font.main=1)
axis(1,col="white",col.axis="yellow")
axis(2,col="white",col.axis="yellow")
abline(lm(y~x),col="red",lwd=3)

Related

outlining statistically significant pixels in plotly (heatmap)

In plotly's heatmap, is it possible to outline specific pixels? In the small reproducible example below, I'd like to know if I can use the matrix defined at the end, called "significant," to add a black outline (with lwd=2) to all pixels with a corresponding value of 1 in 'significant':
library(plotly)
library(RColorBrewer)
m1 <- matrix(c(
-0.0024, -0.0031, -0.0021, -0.0034, -0.0060, -1.00e-02, -8.47e-03, -0.0117, -0.0075, -0.0043, -0.0026, -0.0021,
-0.0015, -0.0076, -0.0032, -0.0105, -0.0107, -2.73e-02, -3.37e-02, -0.0282, -0.0149, -0.0070, -0.0046, -0.0039,
-0.0121, -0.0155, -0.0203, -0.0290, -0.0330, -3.19e-02, -1.74e-02, -0.0103, -0.0084, -0.0180, -0.0162, -0.0136,
-0.0073, -0.0053, -0.0050, -0.0058, -0.0060, -4.38e-03, -2.21e-03, -0.0012, -0.0026, -0.0026, -0.0034, -0.0073,
-0.0027, -0.0031, -0.0054, -0.0069, -0.0071, -6.28e-03, -2.88e-03, -0.0014, -0.0031, -0.0037, -0.0030, -0.0027,
-0.0261, -0.0223, -0.0216, -0.0293, -0.0327, -3.17e-02, -1.77e-02, -0.0084, -0.0059, -0.0060, -0.0120, -0.0157,
0.0045, 0.0006, -0.0031, -0.0058, -0.0093, -9.20e-03, -6.76e-03, -0.0033, 0.0002, 0.0045, 0.0080, 0.0084,
-0.0021, -0.0018, -0.0020, -0.0046, -0.0080, -2.73e-03, 7.43e-04, 0.0004, -0.0010, -0.0017, -0.0022, -0.0024,
-0.0345, -0.0294, -0.0212, -0.0194, -0.0192, -2.25e-02, -2.05e-02, -0.0163, -0.0179, -0.0213, -0.0275, -0.0304,
-0.0034, -0.0038, -0.0040, -0.0045, -0.0059, -1.89e-03, 6.99e-05, -0.0050, -0.0114, -0.0112, -0.0087, -0.0064,
-0.0051, -0.0061, -0.0052, -0.0035, 0.0012, -7.41e-06, -3.43e-03, -0.0055, -0.0020, 0.0016, -0.0024, -0.0069,
-0.0061, -0.0068, -0.0089, -0.0107, -0.0104, -7.65e-03, 2.43e-03, 0.0008, -0.0006, -0.0014, -0.0021, -0.0057,
0.0381, 0.0149, -0.0074, -0.0302, -0.0550, -6.40e-02, -5.28e-02, -0.0326, -0.0114, 0.0121, 0.0367, 0.0501,
-0.0075, -0.0096, -0.0123, -0.0200, -0.0288, -2.65e-02, -2.08e-02, -0.0176, -0.0146, -0.0067, -0.0038, -0.0029,
-0.0154, -0.0162, -0.0252, -0.0299, -0.0350, -3.40e-02, -2.51e-02, -0.0172, -0.0139, -0.0091, -0.0119, -0.0156),
nrow = 15, ncol = 12, byrow=TRUE)
# palette definition
palette <- colorRampPalette(c("darkblue", "blue", "white", "red", "darkred"))
# find max stretch value
zmax1 = max(abs(m1))
plot_ly(
x = c(format(seq(as.Date('2000-10-01'), as.Date('2001-09-30'), by='month'), "%b")),
y = rev(c("TH1", "IN1", "IN3", "GL1", "LH1", "ED9", "TC1", "TC2", "TC3", "UT1", "UT3", "UT5", "GC1", "BC1", "WC1")), ,
z = m1, colors = palette(50), type = "heatmap", width = 700, height = 600, zauto = FALSE, zmin = -1 * zmax1, zmax = zmax1
)
# Can this matrix somehow be used to outline pixels in the heatmap that are equal to one?
# (In this example, the outline pattern will look like a checker board)
significant <- matrix(rep(c(0,1), times=nrow(m1) * ncol(m1) / 2), nrow = 15, ncol = 12)

How to force ggplot to order x-axis or y axis as we want in the plot?

I have a data frame with the first column is like this
df<- structure(list(phenelzine = c(-0.0269, 0.0217, 0.4609, -0.0011,
0.0016, -0.0334, 0.5159, 0.4687, -0.5715, -0.1466, 0.1096, 0.1006,
-0.1021, 0.0093, -0.2616, 0.1496, 0.4463, -0.0833, 0.0573, 0.0602,
0.1345, -0.0911, -0.1444, -0.0624, -0.2009, -0.0579, 0.1701,
-0.161, -0.376, 0.1239, -0.1529, -0.1217, 0.2659, 0.1975, 0.0598,
-0.1397, 0.1959, -0.0342, -0.0771, 0.0017, 0.0562, 0.0605, -0.0976,
0.3257, -0.0385, -0.0687, 0.3087, 0.0992, -0.2253, -0.3171, -0.055,
0.2071, -0.1928, -0.113, -0.2142), denatonium.benzoate = c(-0.1734,
-0.2142, 0.2142, -0.1376, -0.0129, 0.0254, 0.06, 0.1768, 0.2295,
0.1772, 0.1978, -0.0556, 0.0971, 0.0979, 0.2073, 0.061, 0.2782,
-0.048, -0.0825, 0.1922, -0.0395, 0.1594, -0.2117, -0.0999, 5e-04,
-0.0595, -0.2083, 0.1004, -0.1279, -0.0613, -0.0576, -0.0567,
0.1006, -0.0213, -0.1109, 0.0313, 0.0641, -0.2919, -0.0119, 0.1644,
-0.1197, -0.1138, 0.078, -0.2729, -0.022, -0.1864, -0.0709, 0.0211,
0.0183, 0.0175, 0.1655, 0.0064, -0.0701, 0.0274, 0.1163), triamterene = c(-0.0253,
0.2896, 0.1606, -0.086, -0.1886, 0.0355, 0.0552, 0.0733, 0.0131,
0.6887, -0.0161, -0.3962, 0.1294, 0.0316, -0.1851, -0.1193, 0.0308,
-0.1663, 0.0417, -0.0568, 0.1047, 0.0162, 0.3497, 0.0708, -0.0317,
-0.1471, -0.1588, -0.4929, 0.078, 0.1263, -0.2024, -0.0021, -0.3611,
-0.0494, -0.4211, -0.0226, 0.5045, -0.0757, 0.0328, -0.0198,
-0.2622, 0.2297, -0.0454, 0.4094, 0.0826, -0.4326, 0.0316, 0.3048,
-0.2047, 0.1124, -0.2369, 0.1803, -0.1735, 0.2399, -0.0509),
talampicillin = c(-0.1761, -0.0355, 0.0295, 0.1979, 0.0545,
0.0673, -0.0797, -0.1566, 0.0496, 0.2623, -0.197, 0.0192,
-0.2673, 0.0687, -0.0058, -0.4072, -0.06, -0.2315, 0.2532,
-0.0395, 0.0911, -0.1348, -0.018, 0.3084, 0.3751, 0.1659,
-0.1882, 0.1874, -0.0979, -0.0829, -0.1693, 0.0179, -0.0264,
0.1013, 0.4272, 0.1253, -0.0733, 0, 0.1552, -0.3395, -0.0738,
0, 0, -0.1746, -0.2039, 0.2907, 0.0363, 0.2168, -0.1428,
-0.2898, 0.0793, 0.349, -0.043, 0.1547, -0.0557), triamcinolone = c(0.0115,
0.3329, -0.0752, 0.2784, -0.5543, 0.0139, -0.6692, -0.4599,
-4e-04, 0.0115, 0.0624, -0.2127, 0.1339, 0.1186, -0.0732,
0.1033, -0.0672, 0.0038, -0.0445, -0.2484, 0.0075, 0.1113,
0.3911, 0.0205, -0.0126, -0.0763, 0.0073, 0.4081, -0.2826,
-0.0348, 0.0957, -0.0069, 0.0103, 0.0607, 0.7144, 0.0012,
0.0216, 0.1009, -0.0395, -0.0432, 0.08, -0.1039, -0.38, 0.0532,
-0.0404, 0.4977, 0.0735, -0.0793, -0.4312, 0.0332, -0.0964,
0.1067, -0.0468, 0.0052, 0.1366), sulfaphenazole = c(-0.0886,
0.1081, 0.2002, 0.0625, 0.0403, 0.0256, -0.0074, -0.0678,
-0.0393, 0.3201, 0.4213, -0.3058, -0.1228, 0.0797, 0.0591,
-0.0541, -0.0721, -0.1914, -0.3058, 0.4353, 0.176, -0.1903,
0.142, -0.078, 0.0747, -0.3066, 0.2954, -0.2864, 0.0823,
-0.2976, 0.0354, 0.1075, 0.0696, 0.0413, -0.1505, -0.0958,
0.0996, 0.3221, -0.0582, 0.0723, 0.016, -0.3852, 0.0542,
0.0229, 0.1946, -0.0557, -0.0675, -0.2177, 0.2971, 0.3417,
-0.4023, -0.2623, 0.0103, -0.3864, 0.591), procyclidine = c(0.03,
0.0372, 0.335, 0.1666, -0.0048, -0.1153, 0.1449, -0.0488,
0.1038, -0.0245, 0.1008, 0.0194, -0.0315, -0.0325, 0.0161,
0.0316, 0.19, -0.3043, -0.1044, 0.2325, -0.0602, 0.0076,
0.1493, -0.049, 0.0593, -0.0343, 0.0667, 0.1323, 0.2388,
0.0962, -0.2329, -0.2198, 0.0395, -0.0078, 0.1016, 0.03,
-0.1293, -0.0076, -0.1876, -0.2648, 0.0044, 0.0609, 0.0403,
-0.0914, -0.1242, -0.0627, 0.067, 0.0665, 0.1154, 0.286,
-0.2009, 0.2039, -0.0567, -0.0365, -0.0198), pentoxifylline = c(0,
0.3439, -0.0614, 0.0181, -0.0149, -0.0216, -0.1211, -0.1816,
-0.0204, 0.1023, -0.0059, -0.008, -0.1121, 0.2029, 0.052,
-0.0935, 0, 0.0595, 0.0271, -0.0482, 0.0246, -0.1369, 0.1106,
0.4988, -0.0599, 0.0021, -0.0233, 0.2809, 5e-04, -0.0204,
0.0586, 0.0278, 0.0246, 0.0534, 0.0165, -0.1816, -0.071,
-0.0296, -0.1173, 0.0814, -0.0672, 0.0946, -0.2164, 0.0299,
-0.1341, 0.0439, 0.1124, 0.0125, -0.4091, -0.1134, 0.0098,
0.1957, 0.0044, 0.0922, 0.1851), suloctidil = c(-0.0772,
-0.1651, -0.0543, -0.037, 0.2182, -0.1884, 0.1866, 0.2013,
-0.3388, 0.0493, 0.0223, 0.3441, 0.0887, -0.1477, -0.0719,
-0.029, -0.0162, 0.0602, 0.1497, -0.0699, 0.1472, 0.3213,
-0.1266, 0.9143, 0.072, 0.4574, -0.1897, -0.7059, 0.3822,
-0.1055, -0.0744, 0.179, -0.5096, -0.4966, -0.8764, -0.3903,
0.174, 0.2181, -0.122, -0.0097, -0.2281, -0.1387, -0.0506,
0.1179, 0.1911, -0.9006, -0.0161, -0.2298, 0.1777, -0.1341,
-0.0264, -0.3478, -0.188, 0.035, 0.0441), etacrynic.acid = c(0.1017,
-0.4238, -0.0089, -0.1116, 0.1265, -0.0529, -0.121, -0.0243,
-0.0033, -1e-04, 0.0952, 0.4075, -0.3078, 0.1265, -0.0612,
-0.1239, 0.0381, 0.0491, 0.1062, -0.0398, 0.2044, 0.0341,
-0.0654, 0.2705, 0.0408, 0.0064, -0.0858, -0.19, -0.4934,
-0.0524, 2e-04, -0.1496, -0.1018, -0.3303, -0.665, -0.6764,
0, -0.0248, -0.091, 0.052, -0.0327, 0.2288, 0.8196, -0.1288,
0.038, -0.4468, 0.0013, -0.2137, 0.6752, 0.1275, 0.0198,
0.1209, -0.0735, 1e-04, -0.0706), diphenylpyraline = c(0.0495,
-0.1318, -0.0723, -0.0485, 0.0175, -0.1585, 0.0054, 0.0565,
-0.0637, 0.0366, 0.0155, 0.1003, -0.11, -0.129, 0.0673, -0.0519,
0.0284, -0.1663, 0.0224, -0.1806, -0.1265, 0.1559, -0.1337,
-0.0892, 0.08, -0.2713, -0.0064, -0.0193, -0.2862, -0.0627,
0.1242, 0.0607, -0.1815, -0.107, 0.038, -0.0171, 0.1978,
0.1513, -0.1016, -0.086, -0.0019, 0.042, -0.0073, -0.0751,
-0.0388, 0.0844, -0.0678, -0.0556, 0.1765, -0.0377, -0.0143,
0.3352, 0.0206, 0.1197, -0.1429), carbenoxolone = c(0.0769,
0.0987, 0.1992, -0.016, -0.0276, 0.2596, -0.0086, -0.0038,
-0.2432, -0.0237, 0.0696, -0.1436, 0.1942, -0.0411, -0.0948,
0.2645, -0.114, -0.0887, -0.6041, 0.0061, 0.0875, -0.1449,
-0.1735, -0.0606, -0.0785, 0.3483, 0.1196, 0.2659, 0.0614,
-0.1372, 0.1543, 0.0434, -0.0253, -0.0028, 0.0956, 0.3397,
-0.0771, 0.2627, -0.0028, 0.1337, 0.0046, -0.0757, -0.0112,
-0.084, 0.0312, 0.0935, -0.0709, 0.0829, -0.1061, -0.1504,
0.0122, 6e-04, 0.3138, 0.0632, 0.1019), arecoline = c(0.0185,
0.1999, -0.0313, -0.1868, -0.0626, 0.0298, 0.03, 0, -0.2209,
0.0101, -0.0693, -0.1656, -0.1048, 0.2098, 0.0393, -0.1354,
0.0328, -0.0311, -0.1967, -0.2653, 0.204, 0.1737, 0.36, -0.1034,
-0.3326, 0.0613, -0.2044, 0.1967, 0.0042, 0.2329, 0.2409,
-0.0335, 0.0068, 0.5101, 0.2002, 0.1867, 0.2134, -0.1072,
0.0854, 0.2414, -0.0653, 0.3851, 0.1358, -0.0102, 0.0268,
0.2497, -0.1376, 0.1798, 0.0427, 0.1593, -0.29, 0.0343, 0.2249,
-0.1301, -0.0987), chenodeoxycholic.acid = c(-0.0825, 0.2098,
-0.0911, -0.0287, 0.0473, 0.1348, -0.06, -0.0285, -0.1473,
-0.0162, -0.0863, 0.0652, -0.0256, 0.1345, -0.1175, -0.0141,
0.2985, 0.2963, 0.1925, -0.212, -0.2106, -0.1128, -0.3121,
0.0867, 0.0214, 0.0346, 0.0173, 0.1101, -0.3066, 0.1115,
0.0415, 0.285, 0.0787, -0.0985, -0.027, -0.2767, 0.1572,
-0.0518, 0.0815, 0.0168, -0.2047, -0.1517, -0.0076, -0.0359,
0.0596, -0.0706, 0.1006, 0.0099, 0.1661, -0.0435, 0.0331,
0.0996, 0.197, -0.0067, -0.0328), torasemide = c(0.0987,
0.1829, 0.1693, -0.0482, 0.0534, 0.1624, 0.0047, -0.1721,
0.248, 0.1715, -0.2109, -0.0909, 0.0513, -0.1358, 0.6297,
0.0762, -0.3473, -0.2189, -0.126, 0.3054, -0.0451, -0.2243,
0.0914, -0.0199, -6e-04, -0.1102, -0.0082, 0.0242, -0.053,
-0.0825, -0.1874, 0.1251, 0, -0.0457, -0.1179, -0.3169, 0.0559,
0.1999, 0.262, 0.0462, 0.1038, -0.0999, -0.1278, -0.1944,
0.0074, 0.1785, 0.0486, -0.027, -0.2748, -0.0428, 0.0696,
-0.1544, 0.117, 0.1665, 0), troglitazone = c(-0.1513, 0.2568,
0.1377, 0.2474, -0.0359, -0.0859, 0.2014, 0.096, 0.0751,
0.1304, -0.1376, -0.1718, 0.0063, 0.2732, -0.2237, 0.1951,
-0.0496, -0.0087, 0.0245, -0.1212, 0.194, -0.0971, -0.0184,
0.1071, 0.0129, -0.061, 0.1704, -0.0021, 0.3985, 0.0963,
0.1591, -0.381, 0.2277, 0.5395, 0.0611, -0.0204, 0.0614,
-0.2816, 0.0308, -0.0642, -0.1722, -0.0191, -0.0374, 0.0436,
-0.3296, 0.0379, -0.0517, 0.2978, 0.0834, -0.1304, 0.1039,
0.2279, 0.5988, 0.0424, -0.2677), mepenzolate.bromide = c(0.0392,
-0.0041, -0.0531, -0.1213, -0.0919, 0.3096, 0.0545, 0.0922,
0.112, 0.0606, -0.25, -0.0086, 0.2729, 0.1307, 0.2124, -0.039,
-0.1005, 0.0125, 0.0644, -0.0064, 0.0707, 0.1931, -0.5523,
-0.285, -0.3085, 0.0343, 0.0622, -0.1849, -0.0436, 0.1069,
0.072, 0.0312, 0.1016, -0.1611, -0.139, 0.0047, 0.0297, -0.1409,
-0.0834, -0.0087, 0.2839, -0.03, -0.0378, -0.0705, 0.0836,
-0.0824, 0.0803, -0.1378, 0.014, -0.0351, 0.0049, 0.0153,
-0.093, 0.0263, 0.0855), megestrol = c(-0.1106, 0.2547, -0.0488,
0, -0.0406, -0.0826, -0.1795, -0.3099, -0.0316, 0.1563, 0,
-0.1189, -0.0343, -0.0482, 0.8041, 0.5202, 0.0733, 0.0419,
0.2212, -0.0888, 0.0268, 0.0886, -0.0476, -0.3235, -0.1348,
-0.2665, 0.294, 0.122, -0.1695, 0.1186, 0.0927, 0, -0.0429,
-0.0492, 0.0963, -0.0934, 0.1289, 0.1447, -0.0308, -0.1145,
0.1861, -0.0464, 0.0992, 0, 0.0771, -0.1804, 0.0899, 0.1031,
0, 0.1035, 0.1404, 0, -0.1281, -0.2463, -0.2874), dexpropranolol = c(-0.1942,
-0.0051, 0.0561, 0.0166, 0.0029, -0.1707, 0.2173, 0.1178,
-0.0683, -0.2903, -0.2874, 0.1764, -0.1135, 0.2574, 0, -0.1194,
-0.4694, -0.285, 0.0364, -0.0362, 0.158, -0.0648, -0.0046,
0.1435, -0.0946, 0.11, 0.1712, 0.3853, 0.1692, -0.0977, 0.3577,
0.2089, 0.3066, -0.0788, 0.3092, 0.113, -0.1234, 0.5753,
0.0359, 0.1014, 0.2017, 0.2949, 0.019, -0.0855, 0.0428, 0.2171,
-0.0951, -0.0761, -0.1451, -0.2832, -0.2653, -0.166, 0.0376,
-0.0214, 0.0131), nipecotic.acid = c(0.2653, -0.3115, -0.0069,
0.118, -0.0998, -0.0289, 0.1051, 0.0132, -0.0028, -0.1072,
-0.1888, -0.0312, 0.3868, -0.0019, -0.1878, -0.0798, -0.3881,
-0.2162, -0.1189, 0.1569, -0.0537, 0.0196, -0.0013, -0.0818,
-0.1885, 0.2266, 0.2862, 0.1302, 0.0734, 0.0936, -0.0159,
-0.0974, -0.0253, 0.2637, -0.2069, 0.2298, -0.1518, -0.13,
-0.0344, -0.0623, -0.0307, 0.1186, -0.2535, 0.0387, 0.0374,
0.0443, -0.0783, 0.1588, -0.0239, 0.1104, 0.1518, 0.1921,
-0.0744, -0.0125, -0.19), omeprazole = c(0.0272, -0.3796,
-0.0125, 0.0585, -0.1073, -0.0761, 0.3838, 0.5699, 0.0027,
-0.3822, 0.1132, -0.1588, 0.2396, -0.217, 0.0434, 0.1336,
-0.0608, -0.0294, 0.1702, -0.2499, 0.0568, 0.0348, -0.0486,
0, 0.2792, -0.1318, 0.0249, 0.005, 0.1688, -0.3908, -0.2366,
-0.0204, -0.0672, -0.0181, -0.0514, 0.139, 0.0582, 0.109,
0.1018, -0.2249, 0.0432, -0.1882, 0.0818, -0.1082, -0.0456,
-0.0764, 0.4292, 0.0553, -0.1346, -0.2173, 0, 0.1391, 0.1908,
-0.0633, 0.0385), etanidazole = c(-0.1036, 0.0281, 0.0039,
0.0123, -0.2305, -0.0542, 0.0485, -0.0686, -0.1829, 0.2637,
-0.1158, -0.2029, 0.104, 0.3169, 0.1387, 0.0844, -0.1385,
-0.3046, 0.0706, -0.076, -0.1772, 0, -0.393, 0.0841, -0.2469,
-0.1261, 0.1085, 0.0265, 0.0141, 0.0183, 0.2398, -0.0353,
-0.5217, -0.1577, 0.4357, -0.1347, 0.0362, 0.4197, -0.0326,
0.1955, -0.0352, -0.0122, -0.0658, -0.1482, -0.1485, 0.3406,
0.0618, 0.0822, 0.2024, -0.3203, 0.1646, -0.1412, 0.3221,
-8e-04, 0.0472), acenocoumarol = c(-0.0087, 0.2005, -0.1051,
-0.067, -0.0655, -0.0467, -0.4081, -0.1085, -0.0556, 0.0145,
-0.0865, 0.1961, -0.1842, -0.0398, -0.0944, 0.046, 0.0632,
-0.1008, 0.0837, 0.0023, 0.0482, 0.0195, -0.2322, -0.0293,
0.0671, -8e-04, -0.013, -0.0905, -0.0019, -0.0333, 0.0421,
-0.0712, -0.0771, 0.1843, 0.0589, 0.0229, -0.0976, -0.0184,
0.1559, -0.0297, -0.1089, -0.0461, -0.0322, 0.1253, 0.0408,
-0.1147, 0.082, 0.1072, 0.1094, 0.1066, 0.104, 0.1947, 0.1116,
-0.1421, -0.0934), dacarbazine = c(-0.0065, -0.7082, 0.0979,
0.0048, -0.1409, 0.0541, -0.0793, -0.1102, -0.1513, -0.002,
-0.0898, 0.0443, 0.0686, -0.1122, -0.0239, 0.0126, -0.0093,
0.0366, 0.0061, -0.1217, 0.0259, -0.1117, -0.1178, -0.2467,
-0.1128, -0.0671, 0.0347, 0.4719, -0.3849, -0.0517, 0.0764,
0.2058, 0.3147, 0.3275, 0.551, 0.1175, 0.0383, -0.1004, 0.0425,
0.1717, 0.174, 0.0122, -0.1466, 0.0381, -0.0656, 0.2572,
-0.0851, 0.0996, -0.2686, -0.1501, 0.0994, 0.001, 0.0891,
0.0652, -0.2386), diphemanil.metilsulfate = c(-0.0312, -0.2611,
-0.0098, -0.216, 0.24, 0.0909, 0.1171, -0.156, 0.0986, -0.0946,
0.1027, -0.1465, 0.0611, 0.0637, 0.0677, -0.0017, -0.0884,
-0.0023, 0.012, -0.3062, -0.0396, -0.0197, -0.2654, -0.1362,
-0.1075, 0.0738, 0.0039, -0.047, -0.0562, -0.0751, 0.0048,
-0.0273, 0.1636, -0.003, 0.1565, 0.2033, -0.1181, -0.046,
0.0056, 0.0896, -0.0309, -0.0146, -0.0784, 0.002, 0.1111,
0.2156, 0.0915, 0.1174, 0.2337, -0.0151, -0.056, 0.0705,
0.0522, -0.0171, -0.3229), meprylcaine = c(-0.0382, -0.1127,
0, 0, 0.0964, 0.0097, -0.0231, -0.0747, 0.2147, 0.0618, -0.2313,
0.0878, -0.3681, 0.0497, -0.0105, 0.2084, 0.0492, 0.0423,
0.0634, -0.0457, -0.0883, 0.0104, 0.1429, -0.1485, 0.4838,
0.0139, 0.2511, -0.1276, -0.1517, -0.0574, -0.0525, -0.0053,
-0.0796, 0.1029, -0.0393, -0.0587, -0.1787, -0.2193, 0.1723,
0.1684, 0.1708, 0.1961, -0.027, 0.0921, -0.0293, -0.2186,
-0.1013, -0.043, 0.2408, -0.2149, 0.2316, -0.0559, 0.2917,
-0.0128, -0.2173), mevalolactone = c(-0.0393, -0.174, -0.1632,
0.4181, -0.038, 0.1698, -0.1771, -0.168, -0.3952, 0.1739,
0.1304, 0, -0.0317, -0.1822, -0.2021, -0.0743, 0.3155, 0.0782,
0.2533, -0.1159, 0.0135, 0.2274, -0.1785, -0.4384, -0.268,
0.1331, -0.4809, 0.6483, -0.7939, -0.1549, -0.0138, -0.0604,
0.043, 0.1208, 0.4608, 0.4028, 0.1985, 0.1172, 0.0787, 0.099,
-0.0329, 0.1553, -0.0503, -0.1355, 0.0382, 0.4655, -0.1948,
-0.1411, -0.0149, 0.0259, -0.4708, 0.0715, 0.0608, 0, 0.5629
), buspirone = c(-0.1276, -0.0097, -0.1365, 0.0801, -0.0499,
0.0499, 0.2245, 0.0739, -0.0485, -0.0042, -0.2356, -0.1325,
0, 0, -0.0756, 0.0099, 0.069, 0.062, 0.0404, 0.2093, -0.0973,
-0.237, -0.2371, 0.1403, -0.0553, -0.043, 0.0219, 0.0596,
0.0999, -0.1358, 0.1098, -0.06, 0.1429, -0.0758, 0.1528,
-0.0426, 0.1053, 0.2444, -0.0031, -0.2131, -0.1855, 0.144,
0.0037, 0.1078, 0.2742, 0.247, 0.0755, 0.0187, 0.0075, -0.0934,
-0.2814, 0.1086, -0.379, -0.1291, -0.0597), sulfafurazole = c(0.0336,
0.0083, 0.0309, 0.1891, -0.0991, 0.0259, 0.084, 0.0888, 0.0672,
-0.0859, -0.0196, -0.4085, 0.0676, 0.0357, -0.0486, -0.2493,
-0.053, -0.128, 0.103, -0.0471, 0.0839, 0.3382, 0.1353, 0.2906,
0.1022, -0.1326, -0.0457, 0.3148, 0.2374, 0.0719, 0.0469,
-0.2298, 0.1334, 0.1581, -0.1396, -0.2614, -2e-04, 0.0297,
-0.0349, -0.1307, -0.1516, -0.0526, 0.0468, 0.0534, -0.0268,
0.2099, -0.0794, 0.2252, 0.095, -0.1607, 0.1593, 0.0157,
0.0283, 0.1304, -8e-04), ciclopirox = c(0.0958, 0.2534, -0.1897,
-0.0457, 0.1704, -0.2632, -0.2596, -0.1076, 0.3008, 0.1348,
-0.0817, 0.2929, -0.2249, -0.1357, -0.0498, 0.3122, 0.1269,
0.0809, 0.05, -0.2514, -0.3665, -0.1104, 0.0793, 0.8682,
0.3056, 0.2149, -0.3415, 0.1955, 0.2518, -0.1525, 0.0429,
0.4573, -0.556, -0.2508, 0.0437, 0.0459, 0.13, 0.104, 8e-04,
-0.5053, -0.4061, -0.2273, 0.1871, 0.1646, -0.0224, 0.1323,
-0.1473, -0.0917, -0.214, 0.0844, -0.4498, 0.0313, 0.0385,
-0.1485, -0.0553)), .Names = c("phenelzine", "denatonium.benzoate",
"triamterene", "talampicillin", "triamcinolone", "sulfaphenazole",
"procyclidine", "pentoxifylline", "suloctidil", "etacrynic.acid",
"diphenylpyraline", "carbenoxolone", "arecoline", "chenodeoxycholic.acid",
"torasemide", "troglitazone", "mepenzolate.bromide", "megestrol",
"dexpropranolol", "nipecotic.acid", "omeprazole", "etanidazole",
"acenocoumarol", "dacarbazine", "diphemanil.metilsulfate", "meprylcaine",
"mevalolactone", "buspirone", "sulfafurazole", "ciclopirox"), row.names = c("200665_s_at",
"201125_s_at", "201150_s_at", "201162_at", "201560_at", "202133_at",
"202435_s_at", "202436_s_at", "202766_s_at", "203083_at", "203238_s_at",
"203640_at", "204223_at", "204468_s_at", "204589_at", "204619_s_at",
"205381_at", "205422_s_at", "205713_s_at", "205941_s_at", "208626_s_at",
"209581_at", "209747_at", "209875_s_at", "209894_at", "210004_at",
"210078_s_at", "210495_x_at", "210511_s_at", "210517_s_at", "210809_s_at",
"211071_s_at", "211597_s_at", "211709_s_at", "211719_x_at", "212464_s_at",
"212488_at", "212667_at", "213125_at", "213351_s_at", "213352_at",
"213413_at", "213656_s_at", "214770_at", "214927_at", "216442_x_at",
"217428_s_at", "217949_s_at", "218718_at", "219054_at", "219087_at",
"219179_at", "219922_s_at", "222379_at", "37022_at"), class = "data.frame")
I want to heatmap all the columns based on only those rows that have mean of higher than 0.02.
what I do is as follows:
tab <- melt(transform(df, rowname = row.names(df)))
t<- data.frame(sort(rowMeans(df)))
t[t[,1] > 0.02,, drop=FALSE]
library(ggplot2)
ggplot(subset(tab, rowname %in% rownames(t)[t > 0.02]),
aes(x = rowname, y = variable, fill = value)) +
geom_tile() +
scale_fill_gradient2(high="red",mid="white",low="blue") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5))
but it does not do the job, it does put the x axis as it wants not based on the order, for example I want to be from 0.02 to 0.05
so the other looks like
204619_s_at 0.02055667
211709_s_at 0.02357333
216442_x_at 0.02364000
201162_at 0.02389667
217949_s_at 0.03153333
201150_s_at 0.03251000
204468_s_at 0.03279000
211719_x_at 0.03447667
219922_s_at 0.03968667
212667_at 0.04798667
212488_at 0.04833333
209875_s_at 0.05173333
203083_at 0.05493667
210495_x_at 0.05858333
219179_at 0.05932667
in axis and not what it shows

You can try
rn <- rownames(t[t[,1] > 0.02,, drop=FALSE])
tab1 <- subset(tab, rowname %in% rownames(t)[t > 0.02])
tab1$rowname <- factor(tab1$rowname, levels=rn)
library(ggplot2)
ggplot(tab1,aes(x = rowname, y = variable, fill = value)) +
geom_tile() +
scale_fill_gradient2(high="red",mid="white",low="blue") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5))
Or keeping most of the steps within the %>%
library(dplyr)
library(tidyr)
library(ggplot2)
bind_cols(data.frame(rowname=row.names(df)), df) %>%
filter(rowMeans(.[-1]) >0.02) %>%
gather(variable, value,-rowname) %>%
mutate(rowname=factor(rowname, levels=rn)) %>%
ggplot(., aes(x=rowname, y=variable, fill=value))+
geom_tile()+
scale_fill_gradient2(high='red', mid='white', low='blue')+
theme(axis.text.x = element_text(angle = 90, vjust=0.5)) +
xlab('x axis') +
ylab('y axis')

how to select a specific numbers of rows with multiple condition?

I have a data frame like below
df<- structure(list(phenelzine = c(-0.0269, 0.0217, 0.4609, -0.0011,
0.0016, -0.0334, 0.5159, 0.4687, -0.5715, -0.1466, 0.1096, 0.1006,
-0.1021, 0.0093, -0.2616), denatonium.benzoate = c(-0.1734, -0.2142,
0.2142, -0.1376, -0.0129, 0.0254, 0.06, 0.1768, 0.2295, 0.1772,
0.1978, -0.0556, 0.0971, 0.0979, 0.2073), triamterene = c(-0.0253,
0.2896, 0.1606, -0.086, -0.1886, 0.0355, 0.0552, 0.0733, 0.0131,
0.6887, -0.0161, -0.3962, 0.1294, 0.0316, -0.1851), talampicillin = c(-0.1761,
-0.0355, 0.0295, 0.1979, 0.0545, 0.0673, -0.0797, -0.1566, 0.0496,
0.2623, -0.197, 0.0192, -0.2673, 0.0687, -0.0058), triamcinolone = c(0.0115,
0.3329, -0.0752, 0.2784, -0.5543, 0.0139, -0.6692, -0.4599, -4e-04,
0.0115, 0.0624, -0.2127, 0.1339, 0.1186, -0.0732), sulfaphenazole = c(-0.0886,
0.1081, 0.2002, 0.0625, 0.0403, 0.0256, -0.0074, -0.0678, -0.0393,
0.3201, 0.4213, -0.3058, -0.1228, 0.0797, 0.0591), procyclidine = c(0.03,
0.0372, 0.335, 0.1666, -0.0048, -0.1153, 0.1449, -0.0488, 0.1038,
-0.0245, 0.1008, 0.0194, -0.0315, -0.0325, 0.0161), pentoxifylline = c(0,
0.3439, -0.0614, 0.0181, -0.0149, -0.0216, -0.1211, -0.1816,
-0.0204, 0.1023, -0.0059, -0.008, -0.1121, 0.2029, 0.052), suloctidil = c(-0.0772,
-0.1651, -0.0543, -0.037, 0.2182, -0.1884, 0.1866, 0.2013, -0.3388,
0.0493, 0.0223, 0.3441, 0.0887, -0.1477, -0.0719), etacrynic.acid = c(0.1017,
-0.4238, -0.0089, -0.1116, 0.1265, -0.0529, -0.121, -0.0243,
-0.0033, -1e-04, 0.0952, 0.4075, -0.3078, 0.1265, -0.0612), diphenylpyraline = c(0.0495,
-0.1318, -0.0723, -0.0485, 0.0175, -0.1585, 0.0054, 0.0565, -0.0637,
0.0366, 0.0155, 0.1003, -0.11, -0.129, 0.0673), carbenoxolone = c(0.0769,
0.0987, 0.1992, -0.016, -0.0276, 0.2596, -0.0086, -0.0038, -0.2432,
-0.0237, 0.0696, -0.1436, 0.1942, -0.0411, -0.0948), arecoline = c(0.0185,
0.1999, -0.0313, -0.1868, -0.0626, 0.0298, 0.03, 0, -0.2209,
0.0101, -0.0693, -0.1656, -0.1048, 0.2098, 0.0393), chenodeoxycholic.acid = c(-0.0825,
0.2098, -0.0911, -0.0287, 0.0473, 0.1348, -0.06, -0.0285, -0.1473,
-0.0162, -0.0863, 0.0652, -0.0256, 0.1345, -0.1175), torasemide = c(0.0987,
0.1829, 0.1693, -0.0482, 0.0534, 0.1624, 0.0047, -0.1721, 0.248,
0.1715, -0.2109, -0.0909, 0.0513, -0.1358, 0.6297), troglitazone = c(-0.1513,
0.2568, 0.1377, 0.2474, -0.0359, -0.0859, 0.2014, 0.096, 0.0751,
0.1304, -0.1376, -0.1718, 0.0063, 0.2732, -0.2237), mepenzolate.bromide = c(0.0392,
-0.0041, -0.0531, -0.1213, -0.0919, 0.3096, 0.0545, 0.0922, 0.112,
0.0606, -0.25, -0.0086, 0.2729, 0.1307, 0.2124), megestrol = c(-0.1106,
0.2547, -0.0488, 0, -0.0406, -0.0826, -0.1795, -0.3099, -0.0316,
0.1563, 0, -0.1189, -0.0343, -0.0482, 0.8041), dexpropranolol = c(-0.1942,
-0.0051, 0.0561, 0.0166, 0.0029, -0.1707, 0.2173, 0.1178, -0.0683,
-0.2903, -0.2874, 0.1764, -0.1135, 0.2574, 0), nipecotic.acid = c(0.2653,
-0.3115, -0.0069, 0.118, -0.0998, -0.0289, 0.1051, 0.0132, -0.0028,
-0.1072, -0.1888, -0.0312, 0.3868, -0.0019, -0.1878), omeprazole = c(0.0272,
-0.3796, -0.0125, 0.0585, -0.1073, -0.0761, 0.3838, 0.5699, 0.0027,
-0.3822, 0.1132, -0.1588, 0.2396, -0.217, 0.0434), etanidazole = c(-0.1036,
0.0281, 0.0039, 0.0123, -0.2305, -0.0542, 0.0485, -0.0686, -0.1829,
0.2637, -0.1158, -0.2029, 0.104, 0.3169, 0.1387), acenocoumarol = c(-0.0087,
0.2005, -0.1051, -0.067, -0.0655, -0.0467, -0.4081, -0.1085,
-0.0556, 0.0145, -0.0865, 0.1961, -0.1842, -0.0398, -0.0944),
dacarbazine = c(-0.0065, -0.7082, 0.0979, 0.0048, -0.1409,
0.0541, -0.0793, -0.1102, -0.1513, -0.002, -0.0898, 0.0443,
0.0686, -0.1122, -0.0239), diphemanil.metilsulfate = c(-0.0312,
-0.2611, -0.0098, -0.216, 0.24, 0.0909, 0.1171, -0.156, 0.0986,
-0.0946, 0.1027, -0.1465, 0.0611, 0.0637, 0.0677), meprylcaine = c(-0.0382,
-0.1127, 0, 0, 0.0964, 0.0097, -0.0231, -0.0747, 0.2147,
0.0618, -0.2313, 0.0878, -0.3681, 0.0497, -0.0105), mevalolactone = c(-0.0393,
-0.174, -0.1632, 0.4181, -0.038, 0.1698, -0.1771, -0.168,
-0.3952, 0.1739, 0.1304, 0, -0.0317, -0.1822, -0.2021), buspirone = c(-0.1276,
-0.0097, -0.1365, 0.0801, -0.0499, 0.0499, 0.2245, 0.0739,
-0.0485, -0.0042, -0.2356, -0.1325, 0, 0, -0.0756), sulfafurazole = c(0.0336,
0.0083, 0.0309, 0.1891, -0.0991, 0.0259, 0.084, 0.0888, 0.0672,
-0.0859, -0.0196, -0.4085, 0.0676, 0.0357, -0.0486), ciclopirox = c(0.0958,
0.2534, -0.1897, -0.0457, 0.1704, -0.2632, -0.2596, -0.1076,
0.3008, 0.1348, -0.0817, 0.2929, -0.2249, -0.1357, -0.0498
)), .Names = c("phenelzine", "denatonium.benzoate", "triamterene",
"talampicillin", "triamcinolone", "sulfaphenazole", "procyclidine",
"pentoxifylline", "suloctidil", "etacrynic.acid", "diphenylpyraline",
"carbenoxolone", "arecoline", "chenodeoxycholic.acid", "torasemide",
"troglitazone", "mepenzolate.bromide", "megestrol", "dexpropranolol",
"nipecotic.acid", "omeprazole", "etanidazole", "acenocoumarol",
"dacarbazine", "diphemanil.metilsulfate", "meprylcaine", "mevalolactone",
"buspirone", "sulfafurazole", "ciclopirox"), row.names = c("200665_s_at",
"201125_s_at", "201150_s_at", "201162_at", "201560_at", "202133_at",
"202435_s_at", "202436_s_at", "202766_s_at", "203083_at", "203238_s_at",
"203640_at", "204223_at", "204468_s_at", "204589_at"), class = "data.frame")
what I want to do, is after I melt the data, I only keep those that t>0.02 but not all, I want to be able to say, the last 10, or the last 5 or a specific number I like , This should apply on all variables and not only one variable
what i do is as follows:
# sort the mean of the df
t<- data.frame(sort(rowMeans(df)))
# select only those that are higher than 0.02
rn <- rownames(t[t[,1] > 0.02,, drop=FALSE])
# melt the data frame
tab <- melt(transform(df, rowname = row.names(df)))
# select only those that are higher than 0.02
tab1 <- subset(tab, rowname %in% rownames(t)[t > 0.02])

You can use tailto get the last rows of a vector or a data.frame:
tail(tab1 ,5) ## the last five rows
tail(t,5) ## the last five conditions rows

how can I plot one heatmap using two data sets

all existed answers are not working for me! these questions are making the heat maps side by side,
to display two heatmaps in same pdf side by side in R or Side-by-side plots with ggplot2 or others
I have two dfs which I want to plot the 10 highest rows (based on the average) of df1 and 10 lowest rows (based on average) How to force ggplot to order x-axis or y axis as we want in the plot? df1 is taken from the previous post, and df2 is as follows.
df2<- structure(list(phenelzine = c(-0.0665, -0.077, -0.0168, -0.1448,
0.0571, 0.0032, 0.5728, -0.0322, -0.4072, 0.2572, 0.1139, 0.0462,
-0.0317, 0.1378, -0.1963, 0.5325, 0.0716, 0.522, -0.027, 0.3913
), denatonium.benzoate = c(0.0386, -0.1908, -0.1477, 0.0331,
-0.0628, 0.0012, -0.0107, 0.0382, -0.2829, -0.1123, 0.3734, 0.094,
-0.0433, 0.1303, -0.0427, 0.0232, 0.0366, 0.0858, 0.0066, -0.2011
), triamterene = c(-0.0486, 0.3781, -0.0366, 0.2605, -0.1519,
0.5596, 0.0218, -0.2791, 0.3106, 0.0682, -0.0829, 0.1277, -0.1318,
-0.2668, -0.2608, 0.3003, 0.0567, 0.0204, 0.1276, 0.0999), talampicillin = c(0.0064,
0.0735, 0.0215, -0.275, -0.094, 0.2811, 0, -0.033, -0.0238, 0.3376,
-0.3585, 0.1125, 0.0626, 0.0964, 0.0984, -0.1358, 0.0655, -0.2214,
-0.1365, 0.5557), triamcinolone = c(0.0963, 0.2145, 0.1947, -0.0215,
-0.205, 0.0725, 0.1323, -0.0567, 1.0381, 0.0571, 0.0085, -0.0393,
0.1973, 0.0257, -0.0153, 0.0088, 0.07, 0.028, 0.2175, 0.1255),
sulfaphenazole = c(-0.1976, -0.2614, 0.0198, 0.0015, -0.34,
-0.3738, 0.0084, 0.0045, -0.2685, -0.266, 0.0132, 0.0631,
-0.0733, 0.1962, -0.2374, 0.303, -0.0107, -0.0321, 0.0904,
-0.3727), procyclidine = c(0.002, 0.0836, 0.3422, 0.1251,
0.0054, -0.311, -0.1294, -0.1779, 0.0121, -0.1016, -0.1387,
-0.0628, 0.1084, -0.1459, 0.1338, -0.5705, -0.013, 0.0074,
0.0726, -0.1155), pentoxifylline = c(-0.02, 0.0975, 0.1809,
0.0281, -0.1987, -0.1323, -0.0736, 0.0735, 0.1173, 0.0126,
-0.0063, -0.1334, -0.0789, -0.0272, 0.3842, 0.3319, -0.0681,
0.1229, 0.1486, -0.069), suloctidil = c(0.2032, 0.0321, -0.1741,
1.0401, -0.5159, 0.0512, 0.2993, -0.0122, 0.3772, -0.1023,
0.6339, -0.1573, 0.5941, 0.0015, 0.3225, -0.1261, -0.1186,
0.2664, 0.567, 0.0836), etacrynic.acid = c(0.0519, 0.1094,
0.2294, -0.8296, -0.4434, 0.0224, 0.0203, -0.0472, -0.3711,
-0.1684, 0, -0.0868, -0.3012, 0.119, 0.1864, 0.2474, -0.0082,
-0.0043, 0.2668, 0.0415), diphenylpyraline = c(0.1109, -0.248,
-0.0324, -0.0795, 0.0242, 0.1384, 0.0019, -0.0047, -0.112,
0.0233, 0.1739, 0.0804, 0.031, -0.1402, 0.0911, -0.0642,
0.122, 0.3183, -0.0321, -0.0315), carbenoxolone = c(0.0572,
0.0067, -0.0867, 0.0847, -0.0336, 0.1749, -0.0717, 0.0774,
-0.1392, -0.125, -0.2171, 0.0383, 0.2226, -0.1613, 0.4069,
-0.2584, -0.0611, -0.1726, -0.0979, -0.2289), arecoline = c(0.1024,
0.2231, -0.0456, -0.0569, 0.2038, 0.0168, 0.1495, 0.3623,
-0.2502, -0.1069, 0, 0.0973, -0.1981, 0.1, -0.3438, 0.395,
-0.1338, -0.3616, -0.3076, 0.0234), chenodeoxycholic.acid = c(0.0145,
-0.1226, 0.1928, -0.0623, 0.0172, -0.2535, 0.1912, -0.0082,
-0.2637, -0.0639, 0.2127, -0.06, 0.0581, 0.1153, 0.2101,
0.0434, 0.0259, -0.096, -0.0808, -0.0044), torasemide = c(0.0225,
0.1195, 0.1161, 0.0096, 0.2128, 0.2855, -0.1437, -0.2137,
-0.0714, 0.1109, 0.0229, 0.1165, 0.0074, 0.1891, -0.0789,
0.251, 0.0199, -0.3215, 0.0067, -0.143), troglitazone = c(0.1074,
0.1187, 3e-04, 0.1574, 0.3559, 0.0714, -0.1121, -0.1182,
0.1418, 0.196, -0.0248, 0.0437, 0.1814, -0.0927, 0.0938,
-0.0031, -0.0225, 0.0395, 0.0047, 0.14), mepenzolate.bromide = c(-0.1039,
0.0088, 0.2329, 0.0061, 0.0588, -0.0396, -0.1546, 0.1601,
-0.1256, 0.0615, -0.0537, -0.0209, 0.1138, -0.0518, 0.2233,
-0.0858, 0.0073, -0.1966, -0.0476, 0.0741), megestrol = c(0.0256,
0.0967, 0.0533, 0.215, 0.1449, 0.3936, 0.1269, -0.0805, 0.3126,
-0.3387, -0.1375, 0.0675, 0.1531, -0.273, 0.2687, 0.0247,
0.1113, -0.0559, 0.1653, 0.0195), dexpropranolol = c(0.0659,
0.2253, 0.1768, 0.0608, -0.1233, -0.202, -0.1021, -0.0619,
-0.2544, 0.1086, -0.2336, 0.0402, 0.018, -0.4825, -0.1842,
0.6686, 0, -0.0873, -0.0747, 0.2841), nipecotic.acid = c(0.0025,
0.0781, 0.0258, 0.0825, 0.1123, -0.1044, 0.1769, 0.1758,
-0.004, 0.0046, -0.2597, 0.0692, -0.0928, -0.089, -0.0945,
-0.0356, -0.1181, 0.0165, 0.0888, 0.1253), omeprazole = c(0.0172,
0.0859, 0.1016, 0.279, 0.0255, 0.162, 0.0601, -0.0358, 0.1944,
-0.1295, -0.1445, 0.0769, -0.0047, -0.0976, 0.1411, -0.0432,
0.1151, -0.0375, 0.0071, 0.203), etanidazole = c(-0.0776,
-0.0253, 0.1407, 0.2498, -0.0931, 0.0734, -0.0602, -0.1292,
0.2937, 0.052, 0.1856, 0.1195, 0.0524, 0.0944, -0.3275, -0.0198,
0.0598, -0.0356, 0.0854, 0.2093), acenocoumarol = c(0.1362,
0.0303, -0.255, 0.0841, 0.2195, -0.0732, -0.0129, 0.0101,
-0.0939, -0.023, 0.0063, 0.0776, 0.0397, -0.1646, -0.5415,
-0.0177, -0.0949, 0.1158, -0.0037, 0.1216), dacarbazine = c(0.2137,
-0.1382, 0.2363, 0.0733, 0.4311, 0.1098, 0.0351, 0.0831,
-0.3778, 0.3351, 0.058, 0.1463, 0.0753, 0.0238, -0.0843,
0.445, 0.0869, -0.2161, 0.0553, -0.0549), diphemanil.metilsulfate = c(0.0196,
-0.173, 0.0046, 0.0132, -0.0958, -0.0733, 0.0207, 0.0095,
-0.3009, -0.1452, 0.0215, 0.1302, 0.0312, -0.0731, 0.1877,
0.3668, 0.021, -0.0142, -0.3134, -0.0766), meprylcaine = c(-0.0212,
0.0024, 0.0805, -0.1316, 0.0713, -0.1855, 0.2942, 0.0096,
-0.1094, 0.0264, 0.0136, -0.0553, -0.0275, 0, 0.0804, 0.0057,
0.075, 0.338, -0.1472, -0.0797), mevalolactone = c(0.2585,
-0.1235, 0.0609, -0.0379, 0.275, -0.2666, 0.2689, 0.1559,
0.0218, 0.0945, -0.0604, 0.0515, -0.0608, 0.1759, -0.2929,
0.2396, 0.0191, -0.1368, -0.0224, 0.0181), buspirone = c(-0.0704,
-0.1544, -0.0646, 0.0569, -0.1585, 0.4518, -0.252, 0.1089,
-0.1774, 0.0844, -0.1922, -0.0342, 0.0871, -0.2897, 0.4065,
0.2244, 0.1293, -0.1597, -0.0436, 0.1639), sulfafurazole = c(0.2313,
-0.0074, -0.0496, -0.5903, -0.0579, 0.2431, 0.0645, 0.0299,
-0.0586, 0.0226, 0.0898, 0.0175, 0.139, 0.0856, -0.1143,
0.1475, 0.0073, -0.0925, -0.0804, -0.0076), ciclopirox = c(-0.202,
-0.298, 0.2809, -0.7159, -0.7991, 0.0232, -0.0257, -0.0454,
0.8951, 0.6343, 0.4207, -0.2504, -0.4547, 0.2399, 0.0774,
-0.1596, -0.1781, 0.3225, -0.0511, -0.0057)), .Names = c("phenelzine",
"denatonium.benzoate", "triamterene", "talampicillin", "triamcinolone",
"sulfaphenazole", "procyclidine", "pentoxifylline", "suloctidil",
"etacrynic.acid", "diphenylpyraline", "carbenoxolone", "arecoline",
"chenodeoxycholic.acid", "torasemide", "troglitazone", "mepenzolate.bromide",
"megestrol", "dexpropranolol", "nipecotic.acid", "omeprazole",
"etanidazole", "acenocoumarol", "dacarbazine", "diphemanil.metilsulfate",
"meprylcaine", "mevalolactone", "buspirone", "sulfafurazole",
"ciclopirox"), row.names = c("202659_at", "203110_at", "204213_at",
"204279_at", "204301_at", "205049_s_at", "205242_at", "205267_at",
"205476_at", "205891_at", "206641_at", "207076_s_at", "209040_s_at",
"209138_x_at", "209208_at", "209374_s_at", "209397_at", "209569_x_at",
"209970_x_at", "210885_s_at"), class = "data.frame")
from df1, in previous post, we plot the heatmap of those higher than 0.02 (lets say only 10 of them), from df2, I want to plot those that lower than 0.0 threshold but put both images together in one figure
what I do to plot the df1 and df2 is as follows
for df1 that can be taken from link above , I can do as follows
t<- data.frame(sort(rowMeans(df)))
rn <- rownames(t[t[,1] > 0.02,, drop=FALSE])
tab <- melt(transform(df, rowname = row.names(df)))
tab1 <- subset(tab, rowname %in% rownames(t)[t > 0.02])
tab1$rowname <- factor(tab1$rowname, levels=rn)
ggplot(tab1,aes(x = rowname, y = variable, fill = value)) +
geom_tile() +
scale_fill_gradient2(high="black",mid="white",low="darkblue") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5))
To plot the df2 I do as follows
t2<- data.frame(sort(rowMeans(df2)))
rn2 <- rownames(t2[t2[,1] < 0.0,, drop=FALSE])
tabm <- melt(transform(df2, rowname = row.names(df2)))
tab2 <- subset(tabm, rowname %in% rownames(t2)[t2 < 0.0])
tab2$rowname <- factor(tab2$rowname, levels=rn2)
ggplot(tab2,aes(x = rowname, y = variable, fill = value)) +
geom_tile() +
scale_fill_gradient2(high="black",mid="white",low="darkblue") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5))
what I want is to plot the heatmap of both in one image (one part from df1 and the other part from df2)

Here is what I think you are asking for. My df is your dataframe from the earlier question and df2 is from this question.
#calculate mean of each row
df$avg <- apply(df, 1, mean)
df2$avg <- apply(df2, 1, mean)
#add identifier to dataframe to preserve source id after rbind
df$id <- 1
df2$id <- 2
#merge datasets
df3 <- rbind(df, df2)
#add the rownames as a field for preservation after melt
df3$row <- rownames(df3)
#select rows of interest
goodrows <- (df3$id == 1 & df3$avg >= 0.02) | (df3$id == 2 & df3$avg <= 0)
#melt the dataframe retaining only rows of interest
df3m <- melt(df3[goodrows, ], id.vars = c('id', 'avg', 'row'))
#make a new row label that combines "row" and id
df3m$lbl <- paste(df3m$row, "_id_", df3m$id, sep = "")
#plot
ggplot(df3m,aes(x = variable, y = lbl, fill = value)) +
geom_tile() +
scale_fill_gradient2(high="yellow",mid="gray",low="darkblue") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5))

Add 3D abline to cloud plot in R's lattice package

I want to add a 3D abline to a cloud scatterplot in R's lattice package. Here's a subset of my data (3 variables all between 0,1):
dat <- structure(c(0.413, 0.879, 0.016, 0.631, 0.669, 0.048, 1, 0.004, 0.523, 0.001,
0.271, 0.306, 0.014, 0.008, 0.001, 0.023, 0.670, 0.027, 0.291, 0.709,
0.002, 0.003, 0.611, 0.024, 0.580, 0.755, 1, 0.003, 0.038, 0.143, 0.214,
0.161, 0.008, 0.027, 0.109, 0.026, 0.229, 0.006, 0.377, 0.191, 0.724,
0.119, 0.203, 0.002, 0.309, 0.011, 0.141, 0.009, 0.340, 0.152, 0.545,
0.001, 0.217, 0.132, 0.839, 0.052, 0.745, 0.001, 1, 0.273), .Dim = c(20L, 3L))
Here's the cloud plot:
# cloud plot
trellis.par.set("axis.line", list(col="transparent"))
cloud(dat[, 1] ~ dat[, 2] + dat[, 3], pch=16, col="darkorange", groups=NULL, cex=0.8,
screen=list(z = 30, x = -70, y = 0),
scales=list(arrows=FALSE, cex=0.6, col="black", font=3, tck=0.6, distance=1) )
I want to add a dashed grey line between 0,0,0 and 1,1,1 (i.e., diagonally through the plot). I know I can change the points to lines using "type="l", panel.3d.cloud=panel.3dscatter", but I can't see a way to add extra points/lines to the plot using this.
Here's an example of what I want to achieve using scatterplot3d:
# scatterplot3d
s3d <- scatterplot3d(dat, type="p", color="darkorange", angle=55, scale.y=0.7,
pch=16, col.axis="blue", col.grid="lightblue")
# add line
s3d$points3d(c(0,1), c(0,1), c(0,1), col="grey", type="l", lty=2)
I want to do this with a cloud plot to control the angle at which I view the plot (scatterplot3d doesn't allow me to have the 0,0,0 corner of the plot facing). Thanks for any suggestions.

Inelegant and probably fragile, but this seems to work ...
cloud(dat[, 1] ~ dat[, 2] + dat[, 3], pch=16, col="darkorange",
groups=NULL, cex=0.8,
screen=list(z = 30, x = -70, y = 0),
scales=list(arrows=FALSE, cex=0.6, col="black", font=3,
tck=0.6, distance=1) ,
panel=function(...) {
L <- list(...)
L$x <- L$y <- L$z <- c(0,1)
L$type <- "l"
L$col <- "gray"
L$lty <- 2
do.call(panel.cloud,L)
p <- panel.cloud(...)
})
One thing to keep in mind is that this will not do hidden point/line removal, so the line will be either in front of all of the points or behind them all; in this (edited) version, do.call(panel.cloud,L) is first so the points will obscure the line rather than vice versa. If you want hidden line removal then I believe rgl is your only option ... very powerful but not as pretty and with a much more primitive interface.

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