predict.ptw: Prediction of warped signals
In ptw: Parametric Time Warping
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Given a ptw object, predict either the signal at a certain
warped time, or the warped time itself.
Usage
1
2
3
Arguments
object
An object of class "ptw"
newdata
Optional vector or matrix of new data points. If
what equals "response", the new data should be a vector or
matrix of intensities. If what equals "time", the new data is
a vector of time points (a matrix of time points makes no sense...).
what
Either "response", in which case the function returns the
warped signal, or "time", and then the function returns the warped
time axis. That is, the time point in the warped sample
corresponding to the given time point in the original sample.
RTref
Optional vector of retention times in the reference.
...
Further arguments, at the moment not used.
Value
The function returns a matrix (possibly containing only one
row) of either warped time points or signals, warped according to the
warping function defined in object. When warping signals
individually, predict.ptw will check the dimension of
newdata: if this is a vector or a matrix of one row, every
single warping function will be applied to the one row. If the
number of rows equals the number of warping functions, each row will
be warped with its corresponding function. If the number of rows does
not match the number of warping functions and is not equal to one, an
error is given.
Author(s)
Ron Wehrens
References
Eilers, P.H.C. "Parametric Time Warping." Anal. Chem., 2004, 76, 404-411
Bloemberg, T.G. et al. "Improved parametric time warping for
proteomics." Chemom. Intell. Lab. Syst., 2010, 104, pp. 65-74
See Also
Examples
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11
12
13
14
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## educational example, contributed by zeehio (Sergio Oller)
x1 <- c(rep(0, 5), 1,1,1, 20, 40, 20, 1, 1, 1, rep(0, 5))
x2 <- c(rep(0, 6), 1,1,1, 20, 40, 20, 1, 1, 1, rep(0, 4))
time <- 1:length(x1)
## get time-warped object. Default: 'forward' warping, also works
## with backward warping
w1b <- ptw(ref = x1, samp = x2)
## predict intensities of object x2 after warping at the times used in x1
x2wb <- predict(w1b, newdata = x2, what = "response")
## predict times where the original elements of x2 will end up
t2wb <- as.numeric(predict(w1b, newdata = time, what = "time"))
graphics.off()
par(mfrow = c(2,1))
plot(x1, type = "h", col = 2, lwd = 2, main = "Orig data")
points(x2, type = "h", col = 4)
plot(x1, type = "h", col = 2, lwd = 2, main = "Backward warping")
points(c(x2wb), type = "h", col = 4) # what = "response"
points(t2wb, x2, col = 4) # what = "time"
## more relevant example
data(gaschrom)
## Global warping: all samples warped with the same function
ref <- gaschrom[1,]
samp <- gaschrom[14:16,]
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "global")
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
## plot predicted warped signal directly
matlines(t(predict(gp)), lty = 2, col = 1:3)
## plot original signal at warped time axis
matlines(t(predict(gp, newdata = 2001:2600, what = "time")),
t(samp[,2001:2600]), col = 1:3, lwd = 3, lty = 2) ## OK
## result: good alignment with ref, differences between three profiles persist
## Individual warping: all samples warped individually
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "indiv")
predict(gp, what = "time", newdata = 2001:2600)
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
matlines(t(predict(gp, what = "time")),
t(samp), col = 1:3, lty = 2)
## result: each individual profile is aligned to the ref
## How would samples 11:13 be warped using the coefficients from samples
## 14:16 (silly but just to make the point)?
samp.pred <- predict(gp, what = "response", newdata = gaschrom[11:13,])
Example output
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 1996.387 1997.362 1998.336 1999.311 2000.285 2001.260 2002.234 2003.209
[2,] 1999.135 2000.106 2001.078 2002.050 2003.021 2003.993 2004.965 2005.936
[3,] 1994.826 1995.796 1996.765 1997.735 1998.705 1999.674 2000.644 2001.614
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 2004.183 2005.158 2006.133 2007.107 2008.082 2009.056 2010.031 2011.005
[2,] 2006.908 2007.879 2008.851 2009.823 2010.794 2011.766 2012.738 2013.709
[3,] 2002.583 2003.553 2004.522 2005.492 2006.462 2007.431 2008.401 2009.371
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 2011.980 2012.954 2013.929 2014.903 2015.878 2016.852 2017.827 2018.801
[2,] 2014.681 2015.653 2016.624 2017.596 2018.568 2019.539 2020.511 2021.483
[3,] 2010.340 2011.310 2012.279 2013.249 2014.219 2015.188 2016.158 2017.127
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 2019.776 2020.751 2021.725 2022.700 2023.674 2024.649 2025.623 2026.598
[2,] 2022.454 2023.426 2024.398 2025.369 2026.341 2027.312 2028.284 2029.256
[3,] 2018.097 2019.067 2020.036 2021.006 2021.976 2022.945 2023.915 2024.884
[,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
[1,] 2027.572 2028.547 2029.521 2030.496 2031.470 2032.445 2033.419 2034.394
[2,] 2030.227 2031.199 2032.171 2033.142 2034.114 2035.086 2036.057 2037.029
[3,] 2025.854 2026.824 2027.793 2028.763 2029.732 2030.702 2031.672 2032.641
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 2035.369 2036.343 2037.318 2038.292 2039.267 2040.241 2041.216 2042.190
[2,] 2038.001 2038.972 2039.944 2040.916 2041.887 2042.859 2043.831 2044.802
[3,] 2033.611 2034.581 2035.550 2036.520 2037.489 2038.459 2039.429 2040.398
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 2043.165 2044.139 2045.114 2046.088 2047.063 2048.037 2049.012 2049.987
[2,] 2045.774 2046.745 2047.717 2048.689 2049.660 2050.632 2051.604 2052.575
[3,] 2041.368 2042.338 2043.307 2044.277 2045.246 2046.216 2047.186 2048.155
[,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 2050.961 2051.936 2052.910 2053.885 2054.859 2055.834 2056.808 2057.783
[2,] 2053.547 2054.519 2055.490 2056.462 2057.434 2058.405 2059.377 2060.349
[3,] 2049.125 2050.094 2051.064 2052.034 2053.003 2053.973 2054.943 2055.912
[,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72]
[1,] 2058.757 2059.732 2060.706 2061.681 2062.656 2063.630 2064.605 2065.579
[2,] 2061.320 2062.292 2063.263 2064.235 2065.207 2066.178 2067.150 2068.122
[3,] 2056.882 2057.851 2058.821 2059.791 2060.760 2061.730 2062.700 2063.669
[,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80]
[1,] 2066.554 2067.528 2068.503 2069.477 2070.452 2071.426 2072.401 2073.375
[2,] 2069.093 2070.065 2071.037 2072.008 2072.980 2073.952 2074.923 2075.895
[3,] 2064.639 2065.608 2066.578 2067.548 2068.517 2069.487 2070.456 2071.426
[,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88]
[1,] 2074.350 2075.324 2076.299 2077.274 2078.248 2079.223 2080.197 2081.172
[2,] 2076.867 2077.838 2078.810 2079.782 2080.753 2081.725 2082.696 2083.668
[3,] 2072.396 2073.365 2074.335 2075.305 2076.274 2077.244 2078.213 2079.183
[,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 2082.146 2083.121 2084.095 2085.070 2086.044 2087.019 2087.993 2088.968
[2,] 2084.640 2085.611 2086.583 2087.555 2088.526 2089.498 2090.470 2091.441
[3,] 2080.153 2081.122 2082.092 2083.061 2084.031 2085.001 2085.970 2086.940
[,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
[1,] 2089.942 2090.917 2091.892 2092.866 2093.841 2094.815 2095.790 2096.764
[2,] 2092.413 2093.385 2094.356 2095.328 2096.300 2097.271 2098.243 2099.215
[3,] 2087.910 2088.879 2089.849 2090.818 2091.788 2092.758 2093.727 2094.697
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] 2097.739 2098.713 2099.688 2100.662 2101.637 2102.611 2103.586 2104.560
[2,] 2100.186 2101.158 2102.129 2103.101 2104.073 2105.044 2106.016 2106.988
[3,] 2095.667 2096.636 2097.606 2098.575 2099.545 2100.515 2101.484 2102.454
[,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120]
[1,] 2105.535 2106.510 2107.484 2108.459 2109.433 2110.408 2111.382 2112.357
[2,] 2107.959 2108.931 2109.903 2110.874 2111.846 2112.818 2113.789 2114.761
[3,] 2103.423 2104.393 2105.363 2106.332 2107.302 2108.272 2109.241 2110.211
[,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
[1,] 2113.331 2114.306 2115.280 2116.255 2117.229 2118.204 2119.178 2120.153
[2,] 2115.733 2116.704 2117.676 2118.648 2119.619 2120.591 2121.562 2122.534
[3,] 2111.180 2112.150 2113.120 2114.089 2115.059 2116.029 2116.998 2117.968
[,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136]
[1,] 2121.128 2122.102 2123.077 2124.051 2125.026 2126.000 2126.975 2127.949
[2,] 2123.506 2124.477 2125.449 2126.421 2127.392 2128.364 2129.336 2130.307
[3,] 2118.937 2119.907 2120.877 2121.846 2122.816 2123.785 2124.755 2125.725
[,137] [,138] [,139] [,140] [,141] [,142] [,143] [,144]
[1,] 2128.924 2129.898 2130.873 2131.847 2132.822 2133.797 2134.771 2135.746
[2,] 2131.279 2132.251 2133.222 2134.194 2135.166 2136.137 2137.109 2138.081
[3,] 2126.694 2127.664 2128.634 2129.603 2130.573 2131.542 2132.512 2133.482
[,145] [,146] [,147] [,148] [,149] [,150] [,151] [,152]
[1,] 2136.720 2137.695 2138.669 2139.644 2140.618 2141.593 2142.567 2143.542
[2,] 2139.052 2140.024 2140.995 2141.967 2142.939 2143.910 2144.882 2145.854
[3,] 2134.451 2135.421 2136.390 2137.360 2138.330 2139.299 2140.269 2141.239
[,153] [,154] [,155] [,156] [,157] [,158] [,159] [,160]
[1,] 2144.516 2145.491 2146.465 2147.440 2148.415 2149.389 2150.364 2151.338
[2,] 2146.825 2147.797 2148.769 2149.740 2150.712 2151.684 2152.655 2153.627
[3,] 2142.208 2143.178 2144.147 2145.117 2146.087 2147.056 2148.026 2148.996
[,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] 2152.313 2153.287 2154.262 2155.236 2156.211 2157.185 2158.160 2159.134
[2,] 2154.599 2155.570 2156.542 2157.513 2158.485 2159.457 2160.428 2161.400
[3,] 2149.965 2150.935 2151.904 2152.874 2153.844 2154.813 2155.783 2156.752
[,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176]
[1,] 2160.109 2161.083 2162.058 2163.033 2164.007 2164.982 2165.956 2166.931
[2,] 2162.372 2163.343 2164.315 2165.287 2166.258 2167.230 2168.202 2169.173
[3,] 2157.722 2158.692 2159.661 2160.631 2161.601 2162.570 2163.540 2164.509
[,177] [,178] [,179] [,180] [,181] [,182] [,183] [,184]
[1,] 2167.905 2168.880 2169.854 2170.829 2171.803 2172.778 2173.752 2174.727
[2,] 2170.145 2171.117 2172.088 2173.060 2174.032 2175.003 2175.975 2176.946
[3,] 2165.479 2166.449 2167.418 2168.388 2169.358 2170.327 2171.297 2172.266
[,185] [,186] [,187] [,188] [,189] [,190] [,191] [,192]
[1,] 2175.701 2176.676 2177.651 2178.625 2179.600 2180.574 2181.549 2182.523
[2,] 2177.918 2178.890 2179.861 2180.833 2181.805 2182.776 2183.748 2184.720
[3,] 2173.236 2174.206 2175.175 2176.145 2177.114 2178.084 2179.054 2180.023
[,193] [,194] [,195] [,196] [,197] [,198] [,199] [,200]
[1,] 2183.498 2184.472 2185.447 2186.421 2187.396 2188.370 2189.345 2190.319
[2,] 2185.691 2186.663 2187.635 2188.606 2189.578 2190.550 2191.521 2192.493
[3,] 2180.993 2181.963 2182.932 2183.902 2184.871 2185.841 2186.811 2187.780
[,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
[1,] 2191.294 2192.269 2193.243 2194.218 2195.192 2196.167 2197.141 2198.116
[2,] 2193.465 2194.436 2195.408 2196.379 2197.351 2198.323 2199.294 2200.266
[3,] 2188.750 2189.719 2190.689 2191.659 2192.628 2193.598 2194.568 2195.537
[,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216]
[1,] 2199.090 2200.065 2201.039 2202.014 2202.988 2203.963 2204.938 2205.912
[2,] 2201.238 2202.209 2203.181 2204.153 2205.124 2206.096 2207.068 2208.039
[3,] 2196.507 2197.476 2198.446 2199.416 2200.385 2201.355 2202.325 2203.294
[,217] [,218] [,219] [,220] [,221] [,222] [,223] [,224]
[1,] 2206.887 2207.861 2208.836 2209.810 2210.785 2211.759 2212.734 2213.708
[2,] 2209.011 2209.983 2210.954 2211.926 2212.898 2213.869 2214.841 2215.812
[3,] 2204.264 2205.233 2206.203 2207.173 2208.142 2209.112 2210.081 2211.051
[,225] [,226] [,227] [,228] [,229] [,230] [,231] [,232]
[1,] 2214.683 2215.657 2216.632 2217.606 2218.581 2219.556 2220.530 2221.505
[2,] 2216.784 2217.756 2218.727 2219.699 2220.671 2221.642 2222.614 2223.586
[3,] 2212.021 2212.990 2213.960 2214.930 2215.899 2216.869 2217.838 2218.808
[,233] [,234] [,235] [,236] [,237] [,238] [,239] [,240]
[1,] 2222.479 2223.454 2224.428 2225.403 2226.377 2227.352 2228.326 2229.301
[2,] 2224.557 2225.529 2226.501 2227.472 2228.444 2229.416 2230.387 2231.359
[3,] 2219.778 2220.747 2221.717 2222.687 2223.656 2224.626 2225.595 2226.565
[,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248]
[1,] 2230.275 2231.250 2232.224 2233.199 2234.174 2235.148 2236.123 2237.097
[2,] 2232.331 2233.302 2234.274 2235.245 2236.217 2237.189 2238.160 2239.132
[3,] 2227.535 2228.504 2229.474 2230.443 2231.413 2232.383 2233.352 2234.322
[,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256]
[1,] 2238.072 2239.046 2240.021 2240.995 2241.97 2242.944 2243.919 2244.893
[2,] 2240.104 2241.075 2242.047 2243.019 2243.99 2244.962 2245.934 2246.905
[3,] 2235.292 2236.261 2237.231 2238.200 2239.17 2240.140 2241.109 2242.079
[,257] [,258] [,259] [,260] [,261] [,262] [,263] [,264]
[1,] 2245.868 2246.842 2247.817 2248.792 2249.766 2250.741 2251.715 2252.690
[2,] 2247.877 2248.849 2249.820 2250.792 2251.764 2252.735 2253.707 2254.678
[3,] 2243.048 2244.018 2244.988 2245.957 2246.927 2247.897 2248.866 2249.836
[,265] [,266] [,267] [,268] [,269] [,270] [,271] [,272]
[1,] 2253.664 2254.639 2255.613 2256.588 2257.562 2258.537 2259.511 2260.486
[2,] 2255.650 2256.622 2257.593 2258.565 2259.537 2260.508 2261.480 2262.452
[3,] 2250.805 2251.775 2252.745 2253.714 2254.684 2255.654 2256.623 2257.593
[,273] [,274] [,275] [,276] [,277] [,278] [,279] [,280]
[1,] 2261.460 2262.435 2263.410 2264.384 2265.359 2266.333 2267.308 2268.282
[2,] 2263.423 2264.395 2265.367 2266.338 2267.310 2268.282 2269.253 2270.225
[3,] 2258.562 2259.532 2260.502 2261.471 2262.441 2263.410 2264.380 2265.350
[,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288]
[1,] 2269.257 2270.231 2271.206 2272.180 2273.155 2274.129 2275.104 2276.079
[2,] 2271.196 2272.168 2273.140 2274.111 2275.083 2276.055 2277.026 2277.998
[3,] 2266.319 2267.289 2268.259 2269.228 2270.198 2271.167 2272.137 2273.107
[,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296]
[1,] 2277.053 2278.028 2279.002 2279.977 2280.951 2281.926 2282.900 2283.875
[2,] 2278.970 2279.941 2280.913 2281.885 2282.856 2283.828 2284.800 2285.771
[3,] 2274.076 2275.046 2276.016 2276.985 2277.955 2278.924 2279.894 2280.864
[,297] [,298] [,299] [,300] [,301] [,302] [,303] [,304]
[1,] 2284.849 2285.824 2286.798 2287.773 2288.747 2289.722 2290.697 2291.671
[2,] 2286.743 2287.715 2288.686 2289.658 2290.629 2291.601 2292.573 2293.544
[3,] 2281.833 2282.803 2283.772 2284.742 2285.712 2286.681 2287.651 2288.621
[,305] [,306] [,307] [,308] [,309] [,310] [,311] [,312]
[1,] 2292.646 2293.620 2294.595 2295.569 2296.544 2297.518 2298.493 2299.467
[2,] 2294.516 2295.488 2296.459 2297.431 2298.403 2299.374 2300.346 2301.318
[3,] 2289.590 2290.560 2291.529 2292.499 2293.469 2294.438 2295.408 2296.377
[,313] [,314] [,315] [,316] [,317] [,318] [,319] [,320]
[1,] 2300.442 2301.416 2302.391 2303.365 2304.340 2305.315 2306.289 2307.264
[2,] 2302.289 2303.261 2304.233 2305.204 2306.176 2307.148 2308.119 2309.091
[3,] 2297.347 2298.317 2299.286 2300.256 2301.226 2302.195 2303.165 2304.134
[,321] [,322] [,323] [,324] [,325] [,326] [,327] [,328]
[1,] 2308.238 2309.213 2310.187 2311.162 2312.136 2313.111 2314.085 2315.060
[2,] 2310.062 2311.034 2312.006 2312.977 2313.949 2314.921 2315.892 2316.864
[3,] 2305.104 2306.074 2307.043 2308.013 2308.983 2309.952 2310.922 2311.891
[,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336]
[1,] 2316.034 2317.009 2317.983 2318.958 2319.933 2320.907 2321.882 2322.856
[2,] 2317.836 2318.807 2319.779 2320.751 2321.722 2322.694 2323.666 2324.637
[3,] 2312.861 2313.831 2314.800 2315.770 2316.739 2317.709 2318.679 2319.648
[,337] [,338] [,339] [,340] [,341] [,342] [,343] [,344]
[1,] 2323.831 2324.805 2325.780 2326.754 2327.729 2328.703 2329.678 2330.652
[2,] 2325.609 2326.581 2327.552 2328.524 2329.495 2330.467 2331.439 2332.410
[3,] 2320.618 2321.588 2322.557 2323.527 2324.496 2325.466 2326.436 2327.405
[,345] [,346] [,347] [,348] [,349] [,350] [,351] [,352]
[1,] 2331.627 2332.601 2333.576 2334.551 2335.525 2336.500 2337.474 2338.449
[2,] 2333.382 2334.354 2335.325 2336.297 2337.269 2338.240 2339.212 2340.184
[3,] 2328.375 2329.345 2330.314 2331.284 2332.253 2333.223 2334.193 2335.162
[,353] [,354] [,355] [,356] [,357] [,358] [,359] [,360]
[1,] 2339.423 2340.398 2341.372 2342.347 2343.321 2344.296 2345.270 2346.245
[2,] 2341.155 2342.127 2343.099 2344.070 2345.042 2346.014 2346.985 2347.957
[3,] 2336.132 2337.101 2338.071 2339.041 2340.010 2340.980 2341.950 2342.919
[,361] [,362] [,363] [,364] [,365] [,366] [,367] [,368]
[1,] 2347.220 2348.194 2349.169 2350.143 2351.118 2352.092 2353.067 2354.041
[2,] 2348.928 2349.900 2350.872 2351.843 2352.815 2353.787 2354.758 2355.730
[3,] 2343.889 2344.858 2345.828 2346.798 2347.767 2348.737 2349.706 2350.676
[,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376]
[1,] 2355.016 2355.990 2356.965 2357.939 2358.914 2359.888 2360.863 2361.838
[2,] 2356.702 2357.673 2358.645 2359.617 2360.588 2361.560 2362.532 2363.503
[3,] 2351.646 2352.615 2353.585 2354.555 2355.524 2356.494 2357.463 2358.433
[,377] [,378] [,379] [,380] [,381] [,382] [,383] [,384]
[1,] 2362.812 2363.787 2364.761 2365.736 2366.710 2367.685 2368.659 2369.634
[2,] 2364.475 2365.446 2366.418 2367.390 2368.361 2369.333 2370.305 2371.276
[3,] 2359.403 2360.372 2361.342 2362.312 2363.281 2364.251 2365.220 2366.190
[,385] [,386] [,387] [,388] [,389] [,390] [,391] [,392]
[1,] 2370.608 2371.583 2372.557 2373.532 2374.506 2375.481 2376.456 2377.430
[2,] 2372.248 2373.220 2374.191 2375.163 2376.135 2377.106 2378.078 2379.050
[3,] 2367.160 2368.129 2369.099 2370.068 2371.038 2372.008 2372.977 2373.947
[,393] [,394] [,395] [,396] [,397] [,398] [,399] [,400]
[1,] 2378.405 2379.379 2380.354 2381.328 2382.303 2383.277 2384.252 2385.226
[2,] 2380.021 2380.993 2381.965 2382.936 2383.908 2384.879 2385.851 2386.823
[3,] 2374.917 2375.886 2376.856 2377.825 2378.795 2379.765 2380.734 2381.704
[,401] [,402] [,403] [,404] [,405] [,406] [,407] [,408]
[1,] 2386.201 2387.175 2388.150 2389.124 2390.099 2391.074 2392.048 2393.023
[2,] 2387.794 2388.766 2389.738 2390.709 2391.681 2392.653 2393.624 2394.596
[3,] 2382.673 2383.643 2384.613 2385.582 2386.552 2387.522 2388.491 2389.461
[,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416]
[1,] 2393.997 2394.972 2395.946 2396.921 2397.895 2398.870 2399.844 2400.819
[2,] 2395.568 2396.539 2397.511 2398.483 2399.454 2400.426 2401.398 2402.369
[3,] 2390.430 2391.400 2392.370 2393.339 2394.309 2395.279 2396.248 2397.218
[,417] [,418] [,419] [,420] [,421] [,422] [,423] [,424]
[1,] 2401.793 2402.768 2403.742 2404.717 2405.692 2406.666 2407.641 2408.615
[2,] 2403.341 2404.312 2405.284 2406.256 2407.227 2408.199 2409.171 2410.142
[3,] 2398.187 2399.157 2400.127 2401.096 2402.066 2403.035 2404.005 2404.975
[,425] [,426] [,427] [,428] [,429] [,430] [,431] [,432]
[1,] 2409.590 2410.564 2411.539 2412.513 2413.488 2414.462 2415.437 2416.411
[2,] 2411.114 2412.086 2413.057 2414.029 2415.001 2415.972 2416.944 2417.916
[3,] 2405.944 2406.914 2407.884 2408.853 2409.823 2410.792 2411.762 2412.732
[,433] [,434] [,435] [,436] [,437] [,438] [,439] [,440]
[1,] 2417.386 2418.360 2419.335 2420.310 2421.284 2422.259 2423.233 2424.208
[2,] 2418.887 2419.859 2420.831 2421.802 2422.774 2423.745 2424.717 2425.689
[3,] 2413.701 2414.671 2415.641 2416.610 2417.580 2418.549 2419.519 2420.489
[,441] [,442] [,443] [,444] [,445] [,446] [,447] [,448]
[1,] 2425.182 2426.157 2427.131 2428.106 2429.080 2430.055 2431.029 2432.004
[2,] 2426.660 2427.632 2428.604 2429.575 2430.547 2431.519 2432.490 2433.462
[3,] 2421.458 2422.428 2423.397 2424.367 2425.337 2426.306 2427.276 2428.246
[,449] [,450] [,451] [,452] [,453] [,454] [,455] [,456]
[1,] 2432.979 2433.953 2434.928 2435.902 2436.877 2437.851 2438.826 2439.800
[2,] 2434.434 2435.405 2436.377 2437.349 2438.320 2439.292 2440.264 2441.235
[3,] 2429.215 2430.185 2431.154 2432.124 2433.094 2434.063 2435.033 2436.002
[,457] [,458] [,459] [,460] [,461] [,462] [,463] [,464]
[1,] 2440.775 2441.749 2442.724 2443.698 2444.673 2445.647 2446.622 2447.597
[2,] 2442.207 2443.178 2444.150 2445.122 2446.093 2447.065 2448.037 2449.008
[3,] 2436.972 2437.942 2438.911 2439.881 2440.851 2441.820 2442.790 2443.759
[,465] [,466] [,467] [,468] [,469] [,470] [,471] [,472]
[1,] 2448.571 2449.546 2450.520 2451.495 2452.469 2453.444 2454.418 2455.393
[2,] 2449.980 2450.952 2451.923 2452.895 2453.867 2454.838 2455.810 2456.782
[3,] 2444.729 2445.699 2446.668 2447.638 2448.608 2449.577 2450.547 2451.516
[,473] [,474] [,475] [,476] [,477] [,478] [,479] [,480]
[1,] 2456.367 2457.342 2458.316 2459.291 2460.265 2461.240 2462.215 2463.189
[2,] 2457.753 2458.725 2459.697 2460.668 2461.640 2462.611 2463.583 2464.555
[3,] 2452.486 2453.456 2454.425 2455.395 2456.364 2457.334 2458.304 2459.273
[,481] [,482] [,483] [,484] [,485] [,486] [,487] [,488]
[1,] 2464.164 2465.138 2466.113 2467.087 2468.062 2469.036 2470.011 2470.985
[2,] 2465.526 2466.498 2467.470 2468.441 2469.413 2470.385 2471.356 2472.328
[3,] 2460.243 2461.213 2462.182 2463.152 2464.121 2465.091 2466.061 2467.030
[,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496]
[1,] 2471.96 2472.934 2473.909 2474.883 2475.858 2476.833 2477.807 2478.782
[2,] 2473.30 2474.271 2475.243 2476.215 2477.186 2478.158 2479.129 2480.101
[3,] 2468.00 2468.970 2469.939 2470.909 2471.878 2472.848 2473.818 2474.787
[,497] [,498] [,499] [,500] [,501] [,502] [,503] [,504]
[1,] 2479.756 2480.731 2481.705 2482.680 2483.654 2484.629 2485.603 2486.578
[2,] 2481.073 2482.044 2483.016 2483.988 2484.959 2485.931 2486.903 2487.874
[3,] 2475.757 2476.726 2477.696 2478.666 2479.635 2480.605 2481.575 2482.544
[,505] [,506] [,507] [,508] [,509] [,510] [,511] [,512]
[1,] 2487.552 2488.527 2489.501 2490.476 2491.451 2492.425 2493.400 2494.374
[2,] 2488.846 2489.818 2490.789 2491.761 2492.733 2493.704 2494.676 2495.648
[3,] 2483.514 2484.483 2485.453 2486.423 2487.392 2488.362 2489.331 2490.301
[,513] [,514] [,515] [,516] [,517] [,518] [,519] [,520]
[1,] 2495.349 2496.323 2497.298 2498.272 2499.247 2500.221 2501.196 2502.170
[2,] 2496.619 2497.591 2498.562 2499.534 2500.506 2501.477 2502.449 2503.421
[3,] 2491.271 2492.240 2493.210 2494.180 2495.149 2496.119 2497.088 2498.058
[,521] [,522] [,523] [,524] [,525] [,526] [,527] [,528]
[1,] 2503.145 2504.120 2505.094 2506.069 2507.043 2508.018 2508.992 2509.967
[2,] 2504.392 2505.364 2506.336 2507.307 2508.279 2509.251 2510.222 2511.194
[3,] 2499.028 2499.997 2500.967 2501.937 2502.906 2503.876 2504.845 2505.815
[,529] [,530] [,531] [,532] [,533] [,534] [,535] [,536]
[1,] 2510.941 2511.916 2512.890 2513.865 2514.839 2515.814 2516.788 2517.763
[2,] 2512.166 2513.137 2514.109 2515.081 2516.052 2517.024 2517.995 2518.967
[3,] 2506.785 2507.754 2508.724 2509.693 2510.663 2511.633 2512.602 2513.572
[,537] [,538] [,539] [,540] [,541] [,542] [,543] [,544]
[1,] 2518.738 2519.712 2520.687 2521.661 2522.636 2523.610 2524.585 2525.559
[2,] 2519.939 2520.910 2521.882 2522.854 2523.825 2524.797 2525.769 2526.740
[3,] 2514.542 2515.511 2516.481 2517.450 2518.420 2519.390 2520.359 2521.329
[,545] [,546] [,547] [,548] [,549] [,550] [,551] [,552]
[1,] 2526.534 2527.508 2528.483 2529.457 2530.432 2531.406 2532.381 2533.356
[2,] 2527.712 2528.684 2529.655 2530.627 2531.599 2532.570 2533.542 2534.514
[3,] 2522.299 2523.268 2524.238 2525.207 2526.177 2527.147 2528.116 2529.086
[,553] [,554] [,555] [,556] [,557] [,558] [,559] [,560]
[1,] 2534.330 2535.305 2536.279 2537.254 2538.228 2539.203 2540.177 2541.152
[2,] 2535.485 2536.457 2537.428 2538.400 2539.372 2540.343 2541.315 2542.287
[3,] 2530.055 2531.025 2531.995 2532.964 2533.934 2534.904 2535.873 2536.843
[,561] [,562] [,563] [,564] [,565] [,566] [,567] [,568]
[1,] 2542.126 2543.101 2544.075 2545.050 2546.024 2546.999 2547.974 2548.948
[2,] 2543.258 2544.230 2545.202 2546.173 2547.145 2548.117 2549.088 2550.060
[3,] 2537.812 2538.782 2539.752 2540.721 2541.691 2542.660 2543.630 2544.600
[,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576]
[1,] 2549.923 2550.897 2551.872 2552.846 2553.821 2554.795 2555.770 2556.744
[2,] 2551.032 2552.003 2552.975 2553.947 2554.918 2555.890 2556.861 2557.833
[3,] 2545.569 2546.539 2547.509 2548.478 2549.448 2550.417 2551.387 2552.357
[,577] [,578] [,579] [,580] [,581] [,582] [,583] [,584]
[1,] 2557.719 2558.693 2559.668 2560.642 2561.617 2562.592 2563.566 2564.541
[2,] 2558.805 2559.776 2560.748 2561.720 2562.691 2563.663 2564.635 2565.606
[3,] 2553.326 2554.296 2555.266 2556.235 2557.205 2558.174 2559.144 2560.114
[,585] [,586] [,587] [,588] [,589] [,590] [,591] [,592]
[1,] 2565.515 2566.490 2567.464 2568.439 2569.413 2570.388 2571.362 2572.337
[2,] 2566.578 2567.550 2568.521 2569.493 2570.465 2571.436 2572.408 2573.379
[3,] 2561.083 2562.053 2563.022 2563.992 2564.962 2565.931 2566.901 2567.871
[,593] [,594] [,595] [,596] [,597] [,598] [,599] [,600]
[1,] 2573.311 2574.286 2575.261 2576.235 2577.210 2578.184 2579.159 2580.133
[2,] 2574.351 2575.323 2576.294 2577.266 2578.238 2579.209 2580.181 2581.153
[3,] 2568.840 2569.810 2570.779 2571.749 2572.719 2573.688 2574.658 2575.628
ptw documentation built on Jan. 19, 2022, 5:07 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
Given a ptw object, predict either the signal at a certain warped time, or the warped time itself.
Usage
1 2 3 |
Arguments
object |
An object of class "ptw" |
newdata |
Optional vector or matrix of new data points. If
|
what |
Either "response", in which case the function returns the warped signal, or "time", and then the function returns the warped time axis. That is, the time point in the warped sample corresponding to the given time point in the original sample. |
RTref |
Optional vector of retention times in the reference. |
... |
Further arguments, at the moment not used. |
Value
The function returns a matrix (possibly containing only one
row) of either warped time points or signals, warped according to the
warping function defined in object. When warping signals
individually, predict.ptw will check the dimension of
newdata: if this is a vector or a matrix of one row, every
single warping function will be applied to the one row. If the
number of rows equals the number of warping functions, each row will
be warped with its corresponding function. If the number of rows does
not match the number of warping functions and is not equal to one, an
error is given.
Author(s)
Ron Wehrens
References
Eilers, P.H.C. "Parametric Time Warping." Anal. Chem., 2004, 76, 404-411
Bloemberg, T.G. et al. "Improved parametric time warping for proteomics." Chemom. Intell. Lab. Syst., 2010, 104, pp. 65-74
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | ## educational example, contributed by zeehio (Sergio Oller)
x1 <- c(rep(0, 5), 1,1,1, 20, 40, 20, 1, 1, 1, rep(0, 5))
x2 <- c(rep(0, 6), 1,1,1, 20, 40, 20, 1, 1, 1, rep(0, 4))
time <- 1:length(x1)
## get time-warped object. Default: 'forward' warping, also works
## with backward warping
w1b <- ptw(ref = x1, samp = x2)
## predict intensities of object x2 after warping at the times used in x1
x2wb <- predict(w1b, newdata = x2, what = "response")
## predict times where the original elements of x2 will end up
t2wb <- as.numeric(predict(w1b, newdata = time, what = "time"))
graphics.off()
par(mfrow = c(2,1))
plot(x1, type = "h", col = 2, lwd = 2, main = "Orig data")
points(x2, type = "h", col = 4)
plot(x1, type = "h", col = 2, lwd = 2, main = "Backward warping")
points(c(x2wb), type = "h", col = 4) # what = "response"
points(t2wb, x2, col = 4) # what = "time"
## more relevant example
data(gaschrom)
## Global warping: all samples warped with the same function
ref <- gaschrom[1,]
samp <- gaschrom[14:16,]
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "global")
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
## plot predicted warped signal directly
matlines(t(predict(gp)), lty = 2, col = 1:3)
## plot original signal at warped time axis
matlines(t(predict(gp, newdata = 2001:2600, what = "time")),
t(samp[,2001:2600]), col = 1:3, lwd = 3, lty = 2) ## OK
## result: good alignment with ref, differences between three profiles persist
## Individual warping: all samples warped individually
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "indiv")
predict(gp, what = "time", newdata = 2001:2600)
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
matlines(t(predict(gp, what = "time")),
t(samp), col = 1:3, lty = 2)
## result: each individual profile is aligned to the ref
## How would samples 11:13 be warped using the coefficients from samples
## 14:16 (silly but just to make the point)?
samp.pred <- predict(gp, what = "response", newdata = gaschrom[11:13,])
|
Example output
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 1996.387 1997.362 1998.336 1999.311 2000.285 2001.260 2002.234 2003.209
[2,] 1999.135 2000.106 2001.078 2002.050 2003.021 2003.993 2004.965 2005.936
[3,] 1994.826 1995.796 1996.765 1997.735 1998.705 1999.674 2000.644 2001.614
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 2004.183 2005.158 2006.133 2007.107 2008.082 2009.056 2010.031 2011.005
[2,] 2006.908 2007.879 2008.851 2009.823 2010.794 2011.766 2012.738 2013.709
[3,] 2002.583 2003.553 2004.522 2005.492 2006.462 2007.431 2008.401 2009.371
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 2011.980 2012.954 2013.929 2014.903 2015.878 2016.852 2017.827 2018.801
[2,] 2014.681 2015.653 2016.624 2017.596 2018.568 2019.539 2020.511 2021.483
[3,] 2010.340 2011.310 2012.279 2013.249 2014.219 2015.188 2016.158 2017.127
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 2019.776 2020.751 2021.725 2022.700 2023.674 2024.649 2025.623 2026.598
[2,] 2022.454 2023.426 2024.398 2025.369 2026.341 2027.312 2028.284 2029.256
[3,] 2018.097 2019.067 2020.036 2021.006 2021.976 2022.945 2023.915 2024.884
[,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
[1,] 2027.572 2028.547 2029.521 2030.496 2031.470 2032.445 2033.419 2034.394
[2,] 2030.227 2031.199 2032.171 2033.142 2034.114 2035.086 2036.057 2037.029
[3,] 2025.854 2026.824 2027.793 2028.763 2029.732 2030.702 2031.672 2032.641
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 2035.369 2036.343 2037.318 2038.292 2039.267 2040.241 2041.216 2042.190
[2,] 2038.001 2038.972 2039.944 2040.916 2041.887 2042.859 2043.831 2044.802
[3,] 2033.611 2034.581 2035.550 2036.520 2037.489 2038.459 2039.429 2040.398
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 2043.165 2044.139 2045.114 2046.088 2047.063 2048.037 2049.012 2049.987
[2,] 2045.774 2046.745 2047.717 2048.689 2049.660 2050.632 2051.604 2052.575
[3,] 2041.368 2042.338 2043.307 2044.277 2045.246 2046.216 2047.186 2048.155
[,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 2050.961 2051.936 2052.910 2053.885 2054.859 2055.834 2056.808 2057.783
[2,] 2053.547 2054.519 2055.490 2056.462 2057.434 2058.405 2059.377 2060.349
[3,] 2049.125 2050.094 2051.064 2052.034 2053.003 2053.973 2054.943 2055.912
[,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72]
[1,] 2058.757 2059.732 2060.706 2061.681 2062.656 2063.630 2064.605 2065.579
[2,] 2061.320 2062.292 2063.263 2064.235 2065.207 2066.178 2067.150 2068.122
[3,] 2056.882 2057.851 2058.821 2059.791 2060.760 2061.730 2062.700 2063.669
[,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80]
[1,] 2066.554 2067.528 2068.503 2069.477 2070.452 2071.426 2072.401 2073.375
[2,] 2069.093 2070.065 2071.037 2072.008 2072.980 2073.952 2074.923 2075.895
[3,] 2064.639 2065.608 2066.578 2067.548 2068.517 2069.487 2070.456 2071.426
[,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88]
[1,] 2074.350 2075.324 2076.299 2077.274 2078.248 2079.223 2080.197 2081.172
[2,] 2076.867 2077.838 2078.810 2079.782 2080.753 2081.725 2082.696 2083.668
[3,] 2072.396 2073.365 2074.335 2075.305 2076.274 2077.244 2078.213 2079.183
[,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 2082.146 2083.121 2084.095 2085.070 2086.044 2087.019 2087.993 2088.968
[2,] 2084.640 2085.611 2086.583 2087.555 2088.526 2089.498 2090.470 2091.441
[3,] 2080.153 2081.122 2082.092 2083.061 2084.031 2085.001 2085.970 2086.940
[,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
[1,] 2089.942 2090.917 2091.892 2092.866 2093.841 2094.815 2095.790 2096.764
[2,] 2092.413 2093.385 2094.356 2095.328 2096.300 2097.271 2098.243 2099.215
[3,] 2087.910 2088.879 2089.849 2090.818 2091.788 2092.758 2093.727 2094.697
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] 2097.739 2098.713 2099.688 2100.662 2101.637 2102.611 2103.586 2104.560
[2,] 2100.186 2101.158 2102.129 2103.101 2104.073 2105.044 2106.016 2106.988
[3,] 2095.667 2096.636 2097.606 2098.575 2099.545 2100.515 2101.484 2102.454
[,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120]
[1,] 2105.535 2106.510 2107.484 2108.459 2109.433 2110.408 2111.382 2112.357
[2,] 2107.959 2108.931 2109.903 2110.874 2111.846 2112.818 2113.789 2114.761
[3,] 2103.423 2104.393 2105.363 2106.332 2107.302 2108.272 2109.241 2110.211
[,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
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[3,] 2522.299 2523.268 2524.238 2525.207 2526.177 2527.147 2528.116 2529.086
[,553] [,554] [,555] [,556] [,557] [,558] [,559] [,560]
[1,] 2534.330 2535.305 2536.279 2537.254 2538.228 2539.203 2540.177 2541.152
[2,] 2535.485 2536.457 2537.428 2538.400 2539.372 2540.343 2541.315 2542.287
[3,] 2530.055 2531.025 2531.995 2532.964 2533.934 2534.904 2535.873 2536.843
[,561] [,562] [,563] [,564] [,565] [,566] [,567] [,568]
[1,] 2542.126 2543.101 2544.075 2545.050 2546.024 2546.999 2547.974 2548.948
[2,] 2543.258 2544.230 2545.202 2546.173 2547.145 2548.117 2549.088 2550.060
[3,] 2537.812 2538.782 2539.752 2540.721 2541.691 2542.660 2543.630 2544.600
[,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576]
[1,] 2549.923 2550.897 2551.872 2552.846 2553.821 2554.795 2555.770 2556.744
[2,] 2551.032 2552.003 2552.975 2553.947 2554.918 2555.890 2556.861 2557.833
[3,] 2545.569 2546.539 2547.509 2548.478 2549.448 2550.417 2551.387 2552.357
[,577] [,578] [,579] [,580] [,581] [,582] [,583] [,584]
[1,] 2557.719 2558.693 2559.668 2560.642 2561.617 2562.592 2563.566 2564.541
[2,] 2558.805 2559.776 2560.748 2561.720 2562.691 2563.663 2564.635 2565.606
[3,] 2553.326 2554.296 2555.266 2556.235 2557.205 2558.174 2559.144 2560.114
[,585] [,586] [,587] [,588] [,589] [,590] [,591] [,592]
[1,] 2565.515 2566.490 2567.464 2568.439 2569.413 2570.388 2571.362 2572.337
[2,] 2566.578 2567.550 2568.521 2569.493 2570.465 2571.436 2572.408 2573.379
[3,] 2561.083 2562.053 2563.022 2563.992 2564.962 2565.931 2566.901 2567.871
[,593] [,594] [,595] [,596] [,597] [,598] [,599] [,600]
[1,] 2573.311 2574.286 2575.261 2576.235 2577.210 2578.184 2579.159 2580.133
[2,] 2574.351 2575.323 2576.294 2577.266 2578.238 2579.209 2580.181 2581.153
[3,] 2568.840 2569.810 2570.779 2571.749 2572.719 2573.688 2574.658 2575.628
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