Plots an all MS2 fragments distribution along the rt of a given inclusion list entry.
plotRawMS2(struct, ms2id, entryid) # S4 method for RHermesExp,numeric plotRawMS2(struct, ms2id, entryid)
Arguments
| struct | An RHermesExp object |
|---|---|
| ms2id | Number of the MS2Exp object where the spectrum is |
| entryid | Number of the inclusion list entry to plot |
Value
A list of four objects: a plot of the fragments grouped by their mz, a plot of the fragments grouped by their shape similarity, the similarity network and a summary table of peaks found and the group they belong to.
See also
Other plots:
plotFidelity(),
plotSOI(),
plotSS()
Author
Roger Gine
Examples
struct <- readRDS(system.file("extdata", "exampleObject.rds", package = "RHermes")) plotRawMS2(struct, 1, 2)#> $p_bymz#> #> $p_bygroup#> #> $net #> #> $pks #> rt rtmin rtmax into #> 58.064640045166.1 103.51423850 95.32832938 120.14594539 8890341.78061 #> 58.064640045166. 0.00000000 92.34434051 95.32832938 0.00000 #> 58.9528503417969 0.00000000 93.67910261 110.43981498 0.00000 #> 59.0724716186523.1 104.23208032 95.32832938 119.42609474 2031616.31165 #> 59.0724716186523. 0.00000000 92.34434051 95.32832938 0.00000 #> 70.0643539428711 0.00000000 95.32832938 116.86057923 0.00000 #> 117.989807128906 0.00000000 92.34434051 95.32832938 0.00000 #> 118.08553314209.1 102.87612888 95.32832938 120.14594539 20155267.90114 #> 118.08553314209. 0.00000000 92.34434051 95.32832938 0.00000 #> 136.000228881836 0.00000000 90.49537274 94.54436346 0.00000 #> 1 95.32832938 92.34434051 101.45057392 2532811.91008 #> 2 114.05580514 101.45057392 118.70962203 6239938.62013 #> rtmax2 0.00000000 118.70962203 122.30634632 0.00000 #> 11 93.75641003 90.49537274 99.24015234 357610.26248 #> rtmax 0.00000000 101.45057392 118.70962203 0.00000 #> 12 114.05580514 108.44789190 118.70962203 526411.37004 #> 4 0.00000000 95.32832938 108.44789190 0.00000 #> rtmax3 0.00000000 118.70962203 122.30634632 0.00000 #> 13 96.11231298 92.97654210 100.73609845 114623.47560 #> rtmax4 0.00000000 100.73609845 120.14594539 0.00000 #> 14 114.61904040 111.71975318 119.42609474 75820.74913 #> 6 0.00000000 95.32832938 111.71975318 0.00000 #> 15 114.61904040 100.73609845 118.70962203 305958.16107 #> 7 0.00000000 92.97654210 100.73609845 0.00000 #> rtmax6 0.00000000 118.70962203 122.30634632 0.00000 #> 16 96.11231298 93.67910261 110.43981498 188222.19611 #> rtmax7 0.00000000 110.43981498 119.42609474 0.00000 #> 18 0.00000000 92.88689422 101.45057392 0.00000 #> 19 0.00000000 95.32832938 120.14594539 0.00000 #> 110 0.00000000 95.32832938 112.92934224 0.00000 #> 111 0.00000000 97.67223658 112.36359595 0.00000 #> 112 0.00000000 97.67223658 120.14594539 0.00000 #> 113 0.00000000 98.45633405 111.71975318 0.00000 #> 39 0.00000000 92.34434051 95.32832938 0.00000 #> 21 0.00000000 82.60770264 92.34434051 0.00000 #> 23 0.00000000 83.39965966 92.34434051 0.00000 #> 25 0.00000000 82.60770264 92.34434051 0.00000 #> 30 0.00000000 101.45057392 116.86057923 0.00000 #> 35 0.00000000 90.49537274 92.97654210 0.00000 #> 37 0.00000000 89.69702109 93.67910261 0.00000 #> 17 0.00000000 107.09182190 116.86057923 0.00000 #> 3 0.00000000 90.49537274 92.34434051 0.00000 #> 5 0.00000000 86.18742600 92.34434051 0.00000 #> intb maxo sn categ mz members #> 58.064640045166.1 3574897.00270 644818.500000 2 Peak 58.065 1002 #> 58.064640045166. 0.00000 183344.437500 0 Peak 58.065 2 #> 58.9528503417969 0.00000 31047.675781 0 Peak 58.953 1001 #> 59.0724716186523.1 772211.82998 149875.281250 2 Peak 59.072 1002 #> 59.0724716186523. 0.00000 40238.882812 0 Peak 59.072 2 #> 70.0643539428711 0.00000 17625.802734 0 Peak 70.065 1003 #> 117.989807128906 0.00000 29544.457031 0 Peak 117.990 2 #> 118.08553314209.1 8241787.93450 1424987.750000 2 Peak 118.086 1002 #> 118.08553314209. 0.00000 408329.375000 0 Peak 118.086 2 #> 136.000228881836 0.00000 21510.273438 0 Putative 136.000 3 #> 1 304721.64375 423063.468750 1 Peak 72.080 1001 #> 2 1266963.82455 583310.625000 3 Peak 72.080 1003 #> rtmax2 0.00000 391752.562500 0 Putative 72.080 4 #> 11 205112.40136 77930.250000 3 Peak 76.927 1001 #> rtmax 0.00000 16454.802734 0 Peak 76.927 1002 #> 12 141871.02239 72664.546875 3 Peak 55.054 1003 #> 4 0.00000 46375.078125 0 Peak 55.054 1001 #> rtmax3 0.00000 47669.828125 0 Putative 55.054 4 #> 13 34745.39124 26517.703125 5 Peak 76.932 1001 #> rtmax4 0.00000 17848.347656 0 Peak 76.932 1003 #> 14 13631.07209 14212.707031 3 Peak 56.049 1003 #> 6 0.00000 11940.379883 0 Peak 56.049 1002 #> 15 54485.21429 32445.289062 3 Peak 57.057 1003 #> 7 0.00000 23703.085938 0 Peak 57.057 1001 #> rtmax6 0.00000 19837.542969 0 Putative 57.057 4 #> 16 39190.95175 16349.160156 3 Peak 59.930 1001 #> rtmax7 0.00000 11026.972656 0 Peak 59.930 1003 #> 18 0.00000 22005.039062 0 Peak 94.943 1001 #> 19 0.00000 6829.209961 0 Peak 53.038 1003 #> 110 0.00000 30816.642578 0 Peak 58.068 1002 #> 111 0.00000 17711.769531 0 Peak 100.112 1002 #> 112 0.00000 35496.808594 0 Peak 118.122 1002 #> 113 0.00000 19933.611328 0 Peak 58.070 1002 #> 39 0.00000 52104.457031 0 Peak 55.054 1001 #> 21 0.00000 217761.734375 0 Putative 58.065 5 #> 23 0.00000 53398.695312 0 Putative 59.072 5 #> 25 0.00000 469093.187500 0 Putative 118.086 5 #> 30 0.00000 19119.619141 0 Peak 72.085 1003 #> 35 0.00000 21659.679688 0 Putative 100.024 3 #> 37 0.00000 65471.054688 0 Putative 58.953 3 #> 17 0.00000 13727.923828 0 Peak 94.943 1003 #> 3 0.00000 31963.828125 0 Putative 117.990 3 #> 5 0.00000 9673.642578 0 Putative 70.065 5 #>
