Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
plotRegionDescriptionPlots the read density given a chromosome region. UsageplotRegion(bamlist, region, howsmooth = 2, ncounts = NULL, samplenames = NULL) Arguments
ValueReturns the x and y components of the region's reads and plots the density. Author(s)Diana H.P. Low Examplesdata(ssviz) region<-'chr1:3015526-3080526' plotRegion(list(ctrlbam), region=region) Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(ssviz)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: reshape
Attaching package: 'reshape'
The following objects are masked from 'package:S4Vectors':
expand, rename
Loading required package: ggplot2
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ssviz/plotRegion.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotRegion
> ### Title: plotRegion
> ### Aliases: plotRegion
>
> ### ** Examples
>
> data(ssviz)
> region<-'chr1:3015526-3080526'
> plotRegion(list(ctrlbam), region=region)
No counts column provided in bam file. Running unique counts.
Otherwise provide a count matrix or run getCountMatrix.
Processing bam file # 1
| | | 0% | |= | 2% | |== | 3% | |=== | 5% | |===== | 6% | |====== | 8% | |======= | 10% | |======== | 11% | |========= | 13% | |========== | 15% | |=========== | 16% | |============ | 18% | |============== | 19% | |=============== | 21% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |==================== | 29% | |===================== | 31% | |======================= | 32% | |======================== | 34% | |========================= | 35% | |========================== | 37% | |=========================== | 39% | |============================ | 40% | |============================= | 42% | |============================== | 44% | |================================ | 45% | |================================= | 47% | |================================== | 48% | |=================================== | 50% | |==================================== | 52% | |===================================== | 53% | |====================================== | 55% | |======================================== | 56% | |========================================= | 58% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 63% | |============================================= | 65% | |============================================== | 66% | |=============================================== | 68% | |================================================= | 69% | |================================================== | 71% | |=================================================== | 73% | |==================================================== | 74% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 79% | |======================================================== | 81% | |========================================================== | 82% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================= | 87% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 92% | |================================================================= | 94% | |=================================================================== | 95% | |==================================================================== | 97% | |===================================================================== | 98% | |======================================================================| 100%Num reads: 62 Unique positions: 62
[[1]]
[[1]][[1]]
[1] 2990946 2991882 2992818 2993753 2994689 2995625 2996561 2997496 2998432
[10] 2999368 3000304 3001240 3002175 3003111 3004047 3004983 3005918 3006854
[19] 3007790 3008726 3009662 3010597 3011533 3012469 3013405 3014341 3015276
[28] 3016212 3017148 3018084 3019019 3019955 3020891 3021827 3022763 3023698
[37] 3024634 3025570 3026506 3027441 3028377 3029313 3030249 3031185 3032120
[46] 3033056 3033992 3034928 3035863 3036799 3037735 3038671 3039607 3040542
[55] 3041478 3042414 3043350 3044285 3045221 3046157 3047093 3048029 3048964
[64] 3049900 3050836 3051772 3052708 3053643 3054579 3055515 3056451 3057386
[73] 3058322 3059258 3060194 3061130 3062065 3063001 3063937 3064873 3065808
[82] 3066744 3067680 3068616 3069552 3070487 3071423 3072359 3073295 3074230
[91] 3075166 3076102 3077038 3077974 3078909 3079845 3080781 3081717 3082652
[100] 3083588 3084524 3085460 3086396 3087331 3088267 3089203 3090139 3091075
[109] 3092010 3092946 3093882 3094818 3095753 3096689 3097625 3098561 3099497
[118] 3100432 3101368 3102304 3103240 3104175 3105111 3106047
[[2]]
[[2]][[1]]
[1] 16.01595 22.31271 30.79543 41.96924 56.77122 75.87440
[7] 100.43742 131.66275 170.70716 219.56019 279.34185 352.32652
[13] 440.21656 544.85496 668.95882 813.63068 981.95201 1175.04687
[19] 1394.86447 1643.51741 1921.13376 2230.38547 2570.27366 2941.62895
[25] 3344.02824 3775.46735 4235.59484 4720.03567 5225.97317 5748.24402
[31] 6280.93066 6817.13080 7348.75616 7866.37577 8360.39190 8820.59166
[37] 9235.07866 9595.65501 9889.25807 10110.06239 10249.78819 10302.46570
[43] 10268.53721 10142.60358 9932.75880 9641.70210 9278.37808 8854.42695
[49] 8380.04647 7871.52482 7342.21575 6807.66219 6281.91146 5779.22611
[55] 5310.16359 4886.72195 4515.13266 4201.41260 3949.79824 3758.87999
[61] 3631.08631 3560.27609 3543.69571 3575.73802 3649.14973 3759.26770
[67] 3897.50335 4058.55124 4236.00452 4424.54047 4619.82561 4817.86980
[73] 5015.80064 5211.39460 5403.12469 5589.83367 5771.09056 5946.13056
[79] 6114.83622 6276.57273 6430.50260 6575.79025 6710.21358 6832.30954
[85] 6939.01237 7027.28582 7094.09025 7134.56050 7146.34408 7124.51931
[91] 7066.63554 6970.24078 6832.40926 6654.28410 6434.26268 6175.73642
[97] 5881.10866 5554.21796 5201.24849 4826.95074 4439.04544 4043.93214
[103] 3648.66535 3259.56412 2883.24454 2524.15909 2187.32303 1875.68030
[109] 1591.18983 1336.09464 1109.28285 911.56904 740.74287 595.26511
[115] 473.40653 371.92936 289.41202 222.48040 169.16491 127.25678
[121] 94.49785 69.57715 50.54606 36.34874
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> dev.off()
null device
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