Here's a solution using the plyr library:
####################
library(plyr)
dat <- read.table(header=TRUE, sep=",", as.is=TRUE, ###### <---- as.is=TRUE
text="site,tax_name,count,countTotal,countPercentage
CID_1,Cyanobacteria,46295,123509,37.483098398
CID_1,Proteobacteria,36120,123509,29.244832360
CID_1,Bacteroidetes,19546,123509,15.825567368
CID_1,Verrucomicrobia,7886,123509,6.384959801
CID_1,Firmicutes,2843,123509,2.301856545
... <lines deleted here>
CID_9,Armatimonadetes,27,77120,0.035010373
CID_9,Fusobacteria,25,77120,0.032417012
CID_9,Aquificae,13,77120,0.016856846
CID_9,Synergistetes,12,77120,0.015560166
CID_9,Deferribacteres,8,77120,0.010373444
CID_9,Thermotogae,7,77120,0.009076763
CID_9,Chrysiogenetes,3,77120,0.003890041.
")
summ_cid = function(frm) {
# grab at most 6 rows from data frame
toprows = head(frm, 6)
# add a 7th row
toprows[nrow(toprows)+1,] = c(toprows[1,1], "", NA, NA,
sum(toprows$countPercentage))
# all done
return(toprows)
}
result = ddply(dat, "site", summ_cid)
####################
Notes:
1. I needed to add the as.is=TRUE option to read.table()
2. The invocation of ddply() does *not* use summarize()
3. Because there is no use of summarize(), I have not figured out how to use
the dplyr package in this context.
-John
> -----Original Message-----
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Chel Hee
> Lee
> Sent: Sunday, December 07, 2014 11:43 AM
> To: Morway, Eric; R mailing list
> Subject: Re: [R] Condensing data.frame
>
> > datBySite <- split(dat, dat$site)
> > output <- lapply(datBySite, function(x){
> + x$idx <- seq_len(nrow(x))
> + x$grp <- ifelse(x$idx < 7, x$idx, 7)
> + rval <- tapply(x$countPercentage, x$grp, sum) x$grp <- x$count <-
> + x$countTotal <- NULL x <- x[seq_len(7), ] x$tax_name <-
> + as.character(x$tax_name) x$tax_name[7] <- "Others"
> + x$new <- rval
> + return(x)
> + })
> >
> > head(do.call(rbind, output), 14)
> site tax_name countPercentage idx new
> CID_1.1 CID_1 Cyanobacteria 37.483098 1 37.483098
> CID_1.2 CID_1 Proteobacteria 29.244832 2 29.244832
> CID_1.3 CID_1 Bacteroidetes 15.825567 3 15.825567
> CID_1.4 CID_1 Verrucomicrobia 6.384960 4 6.384960
> CID_1.5 CID_1 Firmicutes 2.301857 5 2.301857
> CID_1.6 CID_1 Acidobacteria 2.075152 6 2.075152
> CID_1.7 CID_1 Others 1.675182 7 6.684533
> CID_10.27 CID_10 Proteobacteria 35.366606 1 35.366606
> CID_10.28 CID_10 Bacteroidetes 25.188484 2 25.188484
> CID_10.29 CID_10 Cyanobacteria 23.294828 3 23.294828
> CID_10.30 CID_10 Verrucomicrobia 6.970592 4 6.970592
> CID_10.31 CID_10 Acidobacteria 1.988448 5 1.988448
> CID_10.32 CID_10 Actinobacteria 1.644548 6 1.644548
> CID_10.33 CID_10 Others 1.582823 7 5.546493
> >
>
> I hope this helps.
>
> Chel Hee Lee
>
> On 12/07/2014 08:21 AM, Morway, Eric wrote:
> > Using the dataset "dat" (found below), I'm seeking a way to condense
> > down the data.frame such that each "site" (i.e., "CID_1"..."CID_13")
> > has a maximum of 7 rows of post-processed data, where the first 6 have
> > the highest "countPercentage" and the 7th row is the sum of
> "countPercentage"
> > from all other rows within that "site", and it is assigned the name
> > "Other". So, for the first two sites in the provided data.frame,
> > CID_1 & CID_10, they would reduce to:
> >
> > CID_1 Cyanobacteria 37.48
> > CID_1 Proteobacteria 29.24
> > CID_1 Bacteroidetes 15.83
> > CID_1 Verrucomicrobia 6.38
> > CID_1 Firmicutes 2.30
> > CID_1 Acidobacteria 2.08
> > CID_1 Other 6.68
> > CID_10 Proteobacteria 35.37
> > CID_10 Bacteroidetes 25.19
> > CID_10 Cyanobacteria 23.29
> > CID_10 Verrucomicrobia 6.97
> > CID_10 Acidobacteria 1.99
> > CID_10 Actinobacteria 1.64
> > CID_10 Other 5.55
> >
> >
> > dat <- read.table(header=TRUE, sep=",",
> > text="site,tax_name,count,countTotal,countPercentage
> > CID_1,Cyanobacteria,46295,123509,37.483098398
> > CID_1,Proteobacteria,36120,123509,29.244832360
> > CID_1,Bacteroidetes,19546,123509,15.825567368
> > CID_1,Verrucomicrobia,7886,123509,6.384959801
> > CID_1,Firmicutes,2843,123509,2.301856545
> > CID_1,Acidobacteria,2563,123509,2.075152418
> > CID_1,Actinobacteria,2069,123509,1.675181566
> > CID_1,Planctomycetes,1481,123509,1.199102899
> > CID_1,Chloroflexi,1181,123509,0.956205621
> > CID_1,Gemmatimonadetes,956,123509,0.774032662
> > CID_1,Spirochaetes,688,123509,0.557044426
> > CID_1,Lentisphaerae,526,123509,0.425879895
> > CID_1,Ignavibacteriae,324,123509,0.262329061
> > CID_1,Chlorobi,238,123509,0.192698508
> > CID_1,Nitrospirae,230,123509,0.186221247
> > CID_1,Nitrospinae,169,123509,0.136832134
> > CID_1,Elusimicrobia,131,123509,0.106065145
> > CID_1,Tenericutes,114,123509,0.092300966
> > CID_1,Fibrobacteres,72,123509,0.058295347
> > CID_1,Thermotogae,21,123509,0.017002810
> > CID_1,Fusobacteria,21,123509,0.017002810
> > CID_1,Armatimonadetes,15,123509,0.012144864
> > CID_1,Synergistetes,10,123509,0.008096576
> > CID_1,Deinococcus-Thermus,6,123509,0.004857946
> > CID_1,Deferribacteres,2,123509,0.001619315
> > CID_1,Caldiserica,2,123509,0.001619315
> > CID_10,Proteobacteria,16043,45362,35.366606411
> > CID_10,Bacteroidetes,11426,45362,25.188483753
> > CID_10,Cyanobacteria,10567,45362,23.294828270
> > CID_10,Verrucomicrobia,3162,45362,6.970592126
> > CID_10,Acidobacteria,902,45362,1.988448481
> > CID_10,Actinobacteria,746,45362,1.644548300
> > CID_10,Firmicutes,718,45362,1.582822627
> > CID_10,Gemmatimonadetes,358,45362,0.789206825
> > CID_10,Planctomycetes,357,45362,0.787002337
> > CID_10,Chloroflexi,265,45362,0.584189410
> > CID_10,Spirochaetes,235,45362,0.518054759
> > CID_10,Ignavibacteriae,177,45362,0.390194436
> > CID_10,Lentisphaerae,108,45362,0.238084741
> > CID_10,Nitrospinae,75,45362,0.165336625
> > CID_10,Nitrospirae,58,45362,0.127860324
> > CID_10,Chlorobi,44,45362,0.096997487
> > CID_10,Elusimicrobia,28,45362,0.061725673
> > CID_10,Fibrobacteres,26,45362,0.057316697
> > CID_10,Armatimonadetes,15,45362,0.033067325
> > CID_10,Deinococcus-Thermus,13,45362,0.028658348
> > CID_10,Tenericutes,10,45362,0.022044883
> > CID_10,Synergistetes,9,45362,0.019840395
> > CID_10,Fusobacteria,9,45362,0.019840395
> > CID_10,Deferribacteres,6,45362,0.013226930
> > CID_10,Thermotogae,3,45362,0.006613465
> > CID_10,Caldiserica,2,45362,0.004408977
> > CID_11,Proteobacteria,10019,31387,31.920858954
> > CID_11,Cyanobacteria,8811,31387,28.072131774
> > CID_11,Bacteroidetes,7930,31387,25.265237200
> > CID_11,Verrucomicrobia,1750,31387,5.575556759
> > CID_11,Firmicutes,806,31387,2.567942142
> > CID_11,Acidobacteria,548,31387,1.745945774
> > CID_11,Actinobacteria,434,31387,1.382738076
> > CID_11,Chloroflexi,203,31387,0.646764584
> > CID_11,Planctomycetes,197,31387,0.627648389
> > CID_11,Gemmatimonadetes,192,31387,0.611718227
> > CID_11,Ignavibacteriae,87,31387,0.277184822
> > CID_11,Spirochaetes,80,31387,0.254882595
> > CID_11,Tenericutes,71,31387,0.226208303
> > CID_11,Fusobacteria,67,31387,0.213464173
> > CID_11,Lentisphaerae,54,31387,0.172045751
> > CID_11,Chlorobi,40,31387,0.127441297
> > CID_11,Nitrospinae,33,31387,0.105139070
> > CID_11,Armatimonadetes,22,31387,0.070092714
> > CID_11,Fibrobacteres,15,31387,0.047790487
> > CID_11,Nitrospirae,13,31387,0.041418422
> > CID_11,Elusimicrobia,13,31387,0.041418422
> > CID_11,Deinococcus-Thermus,2,31387,0.006372065
> > CID_12,Cyanobacteria,241,644,37.422360248
> > CID_12,Bacteroidetes,210,644,32.608695652
> > CID_12,Proteobacteria,118,644,18.322981366
> > CID_12,Verrucomicrobia,38,644,5.900621118
> > CID_12,Acidobacteria,11,644,1.708074534
> > CID_12,Ignavibacteriae,6,644,0.931677019
> > CID_12,Lentisphaerae,5,644,0.776397516
> > CID_12,Firmicutes,5,644,0.776397516
> > CID_12,Planctomycetes,3,644,0.465838509
> > CID_12,Fusobacteria,3,644,0.465838509
> > CID_12,Tenericutes,2,644,0.310559006
> > CID_12,Actinobacteria,2,644,0.310559006
> > CID_13,Cyanobacteria,8581,25530,33.611437524
> > CID_13,Bacteroidetes,6878,25530,26.940853897
> > CID_13,Proteobacteria,5341,25530,20.920485703
> > CID_13,Verrucomicrobia,1244,25530,4.872698786
> > CID_13,Firmicutes,1148,25530,4.496670584
> > CID_13,Acidobacteria,548,25530,2.146494320
> > CID_13,Spirochaetes,477,25530,1.868390129
> > CID_13,Ignavibacteriae,298,25530,1.167254211
> > CID_13,Actinobacteria,227,25530,0.889150020
> > CID_13,Planctomycetes,184,25530,0.720720721
> > CID_13,Chloroflexi,181,25530,0.708969839
> > CID_13,Gemmatimonadetes,121,25530,0.473952213
> > CID_13,Lentisphaerae,93,25530,0.364277321
> > CID_13,Tenericutes,61,25530,0.238934587
> > CID_13,Fibrobacteres,47,25530,0.184097141
> > CID_13,Nitrospinae,28,25530,0.109674892
> > CID_13,Nitrospirae,26,25530,0.101840971
> > CID_13,Chlorobi,18,25530,0.070505288
> > CID_13,Elusimicrobia,13,25530,0.050920486
> > CID_13,Synergistetes,8,25530,0.031335684
> > CID_13,Fusobacteria,4,25530,0.015667842
> > CID_13,Deinococcus-Thermus,2,25530,0.007833921
> > CID_13,Thermotogae,2,25530,0.007833921
> > CID_2,Cyanobacteria,43812,94826,46.202518297
> > CID_2,Proteobacteria,22180,94826,23.390209436
> > CID_2,Bacteroidetes,16993,94826,17.920190665
> > CID_2,Verrucomicrobia,4779,94826,5.039757029
> > CID_2,Acidobacteria,1728,94826,1.822285027
> > CID_2,Firmicutes,1385,94826,1.460569886
> > CID_2,Planctomycetes,815,94826,0.859468922
> > CID_2,Actinobacteria,677,94826,0.713939215
> > CID_2,Gemmatimonadetes,625,94826,0.659101934
> > CID_2,Chloroflexi,416,94826,0.438698247
> > CID_2,Spirochaetes,415,94826,0.437643684
> > CID_2,Lentisphaerae,221,94826,0.233058444
> > CID_2,Ignavibacteriae,180,94826,0.189821357
> > CID_2,Fibrobacteres,155,94826,0.163457280
> > CID_2,Chlorobi,112,94826,0.118111067
> > CID_2,Elusimicrobia,111,94826,0.117056503
> > CID_2,Tenericutes,75,94826,0.079092232
> > CID_2,Nitrospinae,40,94826,0.042182524
> > CID_2,Nitrospirae,31,94826,0.032691456
> > CID_2,Deinococcus-Thermus,17,94826,0.017927573
> > CID_2,Armatimonadetes,17,94826,0.017927573
> > CID_2,Synergistetes,16,94826,0.016873010
> > CID_2,Fusobacteria,15,94826,0.015818446
> > CID_2,Deferribacteres,7,94826,0.007381942
> > CID_2,Caldiserica,2,94826,0.002109126
> > CID_2,Thermotogae,2,94826,0.002109126
> > CID_3,Cyanobacteria,18888,46181,40.899937204
> > CID_3,Proteobacteria,12532,46181,27.136701241
> > CID_3,Bacteroidetes,9070,46181,19.640111734
> > CID_3,Verrucomicrobia,2291,46181,4.960914662
> > CID_3,Acidobacteria,689,46181,1.491955566
> > CID_3,Firmicutes,631,46181,1.366362790
> > CID_3,Actinobacteria,470,46181,1.017734566
> > CID_3,Spirochaetes,366,46181,0.792533726
> > CID_3,Planctomycetes,326,46181,0.705918018
> > CID_3,Chloroflexi,282,46181,0.610640740
> > CID_3,Gemmatimonadetes,194,46181,0.420086183
> > CID_3,Fibrobacteres,116,46181,0.251185552
> > CID_3,Ignavibacteriae,109,46181,0.236027804
> > CID_3,Nitrospinae,46,46181,0.099608064
> > CID_3,Nitrospirae,44,46181,0.095277279
> > CID_3,Tenericutes,40,46181,0.086615708
> > CID_3,Lentisphaerae,38,46181,0.082284922
> > CID_3,Chlorobi,16,46181,0.034646283
> > CID_3,Elusimicrobia,14,46181,0.030315498
> > CID_3,Fusobacteria,10,46181,0.021653927
> > CID_3,Armatimonadetes,7,46181,0.015157749
> > CID_3,Synergistetes,2,46181,0.004330785
> > CID_4,Proteobacteria,433,1005,43.084577114
> > CID_4,Bacteroidetes,301,1005,29.950248756
> > CID_4,Actinobacteria,111,1005,11.044776119
> > CID_4,Cyanobacteria,44,1005,4.378109453
> > CID_4,Acidobacteria,28,1005,2.786069652
> > CID_4,Chloroflexi,24,1005,2.388059701
> > CID_4,Nitrospirae,21,1005,2.089552239
> > CID_4,Verrucomicrobia,12,1005,1.194029851
> > CID_4,Gemmatimonadetes,12,1005,1.194029851
> > CID_4,Firmicutes,7,1005,0.696517413
> > CID_4,Spirochaetes,5,1005,0.497512438
> > CID_4,Ignavibacteriae,5,1005,0.497512438
> > CID_4,Elusimicrobia,2,1005,0.199004975
> > CID_5,Proteobacteria,5002,11914,41.984220245
> > CID_5,Bacteroidetes,1512,11914,12.690951821
> > CID_5,Verrucomicrobia,1361,11914,11.423535337
> > CID_5,Acidobacteria,1207,11914,10.130938392
> > CID_5,Cyanobacteria,721,11914,6.051703878
> > CID_5,Planctomycetes,635,11914,5.329864026
> > CID_5,Actinobacteria,398,11914,3.340607688
> > CID_5,Nitrospirae,314,11914,2.635554809
> > CID_5,Chloroflexi,313,11914,2.627161323
> > CID_5,Firmicutes,195,11914,1.636729898
> > CID_5,Gemmatimonadetes,129,11914,1.082759778
> > CID_5,Chlorobi,31,11914,0.260198086
> > CID_5,Armatimonadetes,22,11914,0.184656706
> > CID_5,Ignavibacteriae,21,11914,0.176263220
> > CID_5,Fusobacteria,14,11914,0.117508813
> > CID_5,Deinococcus-Thermus,10,11914,0.083934867
> > CID_5,Lentisphaerae,9,11914,0.075541380
> > CID_5,Elusimicrobia,7,11914,0.058754407
> > CID_5,Nitrospinae,7,11914,0.058754407
> > CID_5,Synergistetes,4,11914,0.033573947
> > CID_5,Spirochaetes,2,11914,0.016786973
> > CID_6,Cyanobacteria,6462,17852,36.197624916
> > CID_6,Proteobacteria,5036,17852,28.209724401
> > CID_6,Bacteroidetes,3906,17852,21.879901412
> > CID_6,Verrucomicrobia,1016,17852,5.691239077
> > CID_6,Acidobacteria,317,17852,1.775711405
> > CID_6,Actinobacteria,286,17852,1.602061394
> > CID_6,Firmicutes,234,17852,1.310777504
> > CID_6,Planctomycetes,134,17852,0.750616177
> > CID_6,Gemmatimonadetes,112,17852,0.627380686
> > CID_6,Spirochaetes,97,17852,0.543356487
> > CID_6,Chloroflexi,77,17852,0.431324221
> > CID_6,Lentisphaerae,56,17852,0.313690343
> > CID_6,Ignavibacteriae,35,17852,0.196056464
> > CID_6,Nitrospirae,23,17852,0.128837105
> > CID_6,Nitrospinae,19,17852,0.106430652
> > CID_6,Tenericutes,12,17852,0.067219359
> > CID_6,Chlorobi,8,17852,0.044812906
> > CID_6,Armatimonadetes,7,17852,0.039211293
> > CID_6,Fibrobacteres,7,17852,0.039211293
> > CID_6,Elusimicrobia,4,17852,0.022406453
> > CID_6,Fusobacteria,2,17852,0.011203227
> > CID_6,Deferribacteres,2,17852,0.011203227
> > CID_7,Cyanobacteria,11046,30425,36.305669680
> > CID_7,Proteobacteria,8418,30425,27.668036154
> > CID_7,Bacteroidetes,6197,30425,20.368118324
> > CID_7,Verrucomicrobia,1745,30425,5.735414955
> > CID_7,Firmicutes,732,30425,2.405916187
> > CID_7,Acidobacteria,582,30425,1.912900575
> > CID_7,Actinobacteria,365,30425,1.199671323
> > CID_7,Fusobacteria,344,30425,1.130649137
> > CID_7,Planctomycetes,253,30425,0.831552999
> > CID_7,Chloroflexi,221,30425,0.726376335
> > CID_7,Gemmatimonadetes,131,30425,0.430566968
> > CID_7,Spirochaetes,127,30425,0.417419885
> > CID_7,Lentisphaerae,88,30425,0.289235826
> > CID_7,Ignavibacteriae,69,30425,0.226787182
> > CID_7,Nitrospinae,37,30425,0.121610518
> > CID_7,Nitrospirae,21,30425,0.069022186
> > CID_7,Chlorobi,17,30425,0.055875103
> > CID_7,Elusimicrobia,15,30425,0.049301561
> > CID_7,Fibrobacteres,9,30425,0.029580937
> > CID_7,Armatimonadetes,4,30425,0.013147083
> > CID_7,Deferribacteres,4,30425,0.013147083
> > CID_8,Cyanobacteria,14446,43589,33.141388883
> > CID_8,Proteobacteria,13270,43589,30.443460506
> > CID_8,Bacteroidetes,8834,43589,20.266581018
> > CID_8,Verrucomicrobia,2529,43589,5.801922503
> > CID_8,Firmicutes,1176,43589,2.697928376
> > CID_8,Acidobacteria,780,43589,1.789442290
> > CID_8,Actinobacteria,542,43589,1.243432976
> > CID_8,Spirochaetes,406,43589,0.931427654
> > CID_8,Planctomycetes,295,43589,0.676776251
> > CID_8,Chloroflexi,277,43589,0.635481429
> > CID_8,Ignavibacteriae,243,43589,0.557480098
> > CID_8,Lentisphaerae,230,43589,0.527656060
> > CID_8,Gemmatimonadetes,162,43589,0.371653399
> > CID_8,Fusobacteria,106,43589,0.243180619
> > CID_8,Tenericutes,57,43589,0.130766937
> > CID_8,Nitrospirae,51,43589,0.117001996
> > CID_8,Chlorobi,50,43589,0.114707839
> > CID_8,Nitrospinae,36,43589,0.082589644
> > CID_8,Fibrobacteres,34,43589,0.078001331
> > CID_8,Elusimicrobia,29,43589,0.066530547
> > CID_8,Armatimonadetes,19,43589,0.043588979
> > CID_8,Aquificae,8,43589,0.018353254
> > CID_8,Deferribacteres,7,43589,0.016059097
> > CID_8,Dictyoglomi,2,43589,0.004588314
> > CID_9,Proteobacteria,26463,77120,34.314056017
> > CID_9,Cyanobacteria,20329,77120,26.360217842
> > CID_9,Bacteroidetes,15956,77120,20.689834025
> > CID_9,Verrucomicrobia,3323,77120,4.308869295
> > CID_9,Firmicutes,2726,77120,3.534751037
> > CID_9,Spirochaetes,1644,77120,2.131742739
> > CID_9,Acidobacteria,1634,77120,2.118775934
> > CID_9,Actinobacteria,1200,77120,1.556016598
> > CID_9,Chloroflexi,1128,77120,1.462655602
> > CID_9,Planctomycetes,872,77120,1.130705394
> > CID_9,Ignavibacteriae,578,77120,0.749481328
> > CID_9,Lentisphaerae,264,77120,0.342323651
> > CID_9,Gemmatimonadetes,263,77120,0.341026971
> > CID_9,Fibrobacteres,170,77120,0.220435685
> > CID_9,Nitrospirae,148,77120,0.191908714
> > CID_9,Nitrospinae,136,77120,0.176348548
> > CID_9,Chlorobi,74,77120,0.095954357
> > CID_9,Tenericutes,71,77120,0.092064315
> > CID_9,Elusimicrobia,46,77120,0.059647303
> > CID_9,Armatimonadetes,27,77120,0.035010373
> > CID_9,Fusobacteria,25,77120,0.032417012
> > CID_9,Aquificae,13,77120,0.016856846
> > CID_9,Synergistetes,12,77120,0.015560166
> > CID_9,Deferribacteres,8,77120,0.010373444
> > CID_9,Thermotogae,7,77120,0.009076763
> > CID_9,Chrysiogenetes,3,77120,0.003890041
> > ")
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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