Creating custom import functions

Source: vignettes/custom-import-function.Rmd

When eemR was originally created, I wrote few functions to import eems derived from the spectrofluorometers I knew. Given the high diversity in file formats, eemR now offers the possibility for the user to write his/her own import function.

An example

In this example, we will learn how to create a import function for a specific eem file generated by the software of a Cary Eclipse spectrofluorometer. First, lets have a look to the content of custom_cary.csv.

file <- system.file("extdata/custom_cary.csv", package = "eemR")

cat(readLines(file, n = 25), sep = "\n")
Wavelength (nm),Intensity (a.u.),Z Axis,
,01_SYN_50.00,01_SYN_55.00,01_SYN_60.00,01_SYN_65.00,01_SYN_70.00,01_SYN_75.00,01_SYN_80.00,01_SYN_85.00,01_SYN_90.00,01_SYN_95.00,01_SYN_100.00,01_SYN_105.00,01_SYN_110.00,01_SYN_115.00,01_SYN_120.00,01_SYN_125.00,01_SYN_130.00,01_SYN_135.00,01_SYN_140.00,01_SYN_145.00,01_SYN_150.00,01_SYN_155.00,01_SYN_160.00,01_SYN_165.00,01_SYN_170.00,01_SYN_175.00,01_SYN_180.00,01_SYN_185.00,01_SYN_190.00,01_SYN_195.00,01_SYN_200.00,01_SYN_205.00,01_SYN_210.00,01_SYN_215.00,01_SYN_220.00,01_SYN_225.00,01_SYN_230.00,01_SYN_235.00,01_SYN_240.00,01_SYN_245.00,01_SYN_250.00,01_SYN_255.00,01_SYN_260.00,01_SYN_265.00,01_SYN_270.00,01_SYN_275.00,01_SYN_280.00,01_SYN_285.00,01_SYN_290.00,01_SYN_295.00,01_SYN_300.00,01_SYN_305.00,01_SYN_310.00,01_SYN_315.00,01_SYN_320.00,01_SYN_325.00,01_SYN_330.00
,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57
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262.029998779297,3.82153797149658,4.68460035324097,5.47021532058716,6.31838464736938,7.08445405960083,8.41258716583252,9.51007556915283,11.8409414291382,14.6743392944336,18.2979602813721,21.9991550445557,27.3488578796387,32.1398429870605,37.7207489013672,41.5274200439453,47.5885772705078,51.7020034790039,57.099292755127,61.7406425476074,65.6555023193359,69.953987121582,71.0863876342773,72.1729507446289,74.046012878418,76.3831253051758,76.5245666503906,78.6100769042969,78.930061340332,78.9697952270508,78.8229598999023,77.4386367797852,74.3858337402344,72.0304260253906,69.0096817016602,64.5219955444336,61.5817642211914,57.9443168640137,54.1362762451172,50.5893630981445,47.3394966125488,43.4472389221191,49.5518836975098,97.0061645507812,81.2925109863281,47.1760177612305,29.0424575805664,26.0920829772949,23.7819023132324,20.9830074310303,19.6952857971191,17.1577033996582,16.684419631958,16.3815746307373,15.3087348937988,13.0794944763184,10.3042526245117,8.92405891418457
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278,8.48977661132813,9.72201824188232,10.9945764541626,12.3502340316772,14.6449317932129,16.5595989227295,18.747974395752,21.2034740447998,24.3064498901367,27.6277103424072,30.4052429199219,33.8209686279297,36.1396217346191,39.385196685791,42.7643585205078,45.4900398254395,47.948673248291,49.6876640319824,50.9636993408203,52.3083076477051,53.5917663574219,54.0611381530762,55.3604202270508,55.7568016052246,56.2939567565918,57.7520179748535,56.8129348754883,56.0606842041016,55.2115783691406,53.1221351623535,50.9379577636719,49.4548149108887,46.8170204162598,44.3587074279785,41.6488952636719,39.3058090209961,36.089183807373,33.8585624694824,31.6063346862793,29.3909339904785,27.0542392730713,24.8800773620605,22.6839694976807,21.0330677032471,21.5759353637695,46.9133758544922,73.185661315918,49.4711151123047,17.0408706665039,11.9908084869385,10.5606393814087,9.47162628173828,8.83677864074707,8.19705486297607,7.32574367523193,6.79376029968262,6.77574682235718
280,9.17060279846191,10.7361602783203,11.9468517303467,13.7060613632202,15.5742597579956,18.0546531677246,20.4713668823242,23.7345409393311,26.4405708312988,29.5096549987793,32.8378601074219,34.5172424316406,38.207218170166,41.8863258361816,44.4178733825684,47.1293525695801,49.3283500671387,50.4015922546387,51.2054824829102,52.1976928710937,53.2793464660645,54.1178741455078,54.5313758850098,54.9432258605957,55.8546295166016,55.7861747741699,55.2872047424316,54.3410720825195,53.1083488464355,51.0687599182129,48.7317733764648,46.8424453735352,44.4959030151367,42.7631225585937,39.6353950500488,37.2586402893066,34.5268287658691,32.335823059082,30.0511512756348,27.9724884033203,25.4165897369385,22.9819965362549,21.0822505950928,19.606632232666,18.7149105072021,29.8068771362305,64.5562973022461,67.0754699707031,25.1678047180176,11.4009189605713,9.83836936950684,9.01907253265381,8.37013435363769,7.81657075881958,7.19332599639893,6.66719484329224,6.11242961883545
282,10.1019287109375,11.5800104141235,12.9970426559448,14.8697080612183,16.7626628875732,19.2185344696045,21.8908138275146,24.7509365081787,27.8465919494629,31.2070140838623,34.1463890075684,37.0135650634766,39.6970901489258,43.4160842895508,45.342357635498,47.8797187805176,49.8394889831543,50.3688507080078,50.4839782714844,52.2149238586426,52.8301200866699,53.2352714538574,54.1411628723145,54.8820114135742,54.8560218811035,55.3460540771484,53.9031372070313,53.0047569274902,51.1480407714844,49.4790000915527,46.8833351135254,44.6873245239258,42.497917175293,39.9358444213867,37.9777565002441,35.3452682495117,32.9601249694824,30.4906444549561,28.3763179779053,26.1937122344971,24.0974254608154,21.8326168060303,20.3651542663574,18.9013957977295,17.3187465667725,18.7819938659668,53.0021514892578,71.5673294067383,42.6870040893555,12.9425649642944,9.78479480743408,8.45710563659668,7.94507169723511,7.23891258239746,6.70252704620361,6.16295576095581,5.49235391616821
284,10.4421472549438,12.0179777145386,13.8513479232788,16.1304492950439,18.0575847625732,20.7996673583984,24.1695022583008,26.6093864440918,30.0439910888672,32.5205383300781,35.3260383605957,38.5231170654297,41.2779159545898,44.2526016235352,46.2045631408691,48.5946846008301,50.4220352172852,50.7044219970703,51.5091133117676,51.6817779541016,53.2729721069336,52.9527969360352,53.5108604431152,53.4884338378906,54.0079193115234,53.1847801208496,52.2562294006348,50.9408912658691,48.9856147766113,47.726390838623,44.9403762817383,42.6372413635254,40.4396896362305,38.6279335021973,36.564884185791,33.3923530578613,31.1226139068604,29.0496425628662,26.8141498565674,25.467809677124,23.0671539306641,20.7443943023682,19.1811771392822,17.7717571258545,15.8602781295776,15.4107141494751,35.026912689209,67.0927581787109,60.3559799194336,18.6382484436035,9.50141620635986,8.14902019500732,7.78250789642334,6.95368623733521,6.33366012573242,5.82480907440186,5.3531494140625
286,11.1862163543701,12.5576801300049,14.7683629989624,17.4937152862549,19.7286758422852,22.4737720489502,25.3906593322754,28.5470027923584,31.3895568847656,34.1828346252441,36.8001937866211,40.9202270507812,42.842700958252,45.3932800292969,48.1626968383789,49.2899055480957,50.6819648742676,51.6555786132812,50.9963874816895,51.641471862793,52.2208023071289,52.3825531005859,52.6477203369141,52.536060333252,53.2410163879395,51.7915420532227,50.9816284179687,49.817985534668,48.2453765869141,45.4916687011719,42.9353523254395,40.9983291625977,39.0420150756836,36.6315498352051,34.1375885009766,31.8135585784912,29.7591304779053,27.8124866485596,25.1664371490479,23.2535800933838,21.4422187805176,19.5025844573975,18.1085643768311,16.3618869781494,15.3263788223267,13.9953851699829,21.2125186920166,59.00048828125,67.0372848510742,28.2929344177246,9.06644630432129,7.53646755218506,7.2679705619812,6.53416347503662,5.90030336380005,5.24513149261475,5.02353954315186
288,11.418137550354,13.4024925231934,16.1324062347412,18.5914611816406,20.8604259490967,24.2508201599121,27.0655269622803,30.1565170288086,33.5743141174316,36.5337982177734,38.3620414733887,41.7550888061523,45.4048347473145,47.3766479492188,49.3450202941895,50.6066551208496,51.1274299621582,51.0591278076172,51.7542839050293,51.8490257263184,52.4329261779785,52.7435836791992,51.958667755127,52.1096992492676,51.6449012756348,50.8255767822266,49.5630569458008,48.119441986084,45.8649291992188,43.289966583252,41.3925895690918,39.0771675109863,37.5333633422852,35.1679000854492,32.8708381652832,30.4508457183838,28.3584594726562,26.4721431732178,24.2980518341064,22.1344432830811,20.2115783691406,18.611270904541,17.2335796356201,15.7603769302368,14.0518999099731,13.3108510971069,14.1540794372559,42.4813041687012,63.6471290588379,45.0498695373535,10.7297897338867,7.17738008499145,6.67493677139282,6.13038015365601,5.46122550964355,5.14815235137939,4.59314632415771
290,12.3915195465088,14.5368547439575,16.925220489502,19.987886428833,22.2329254150391,25.9109668731689,28.910343170166,32.4790954589844,35.4773635864258,38.0293235778809,40.3983268737793,43.6618843078613,46.437801361084,49.0418014526367,50.770393371582,51.6063423156738,51.665714263916,52.2079315185547,52.2347183227539,52.7055702209473,52.302661895752,52.0769920349121,52.2918472290039,52.1205558776855,51.725341796875,50.3940391540527,48.1075820922852,46.3073348999023,44.0949325561523,42.2608528137207,40.0914421081543,37.5530967712402,35.2090759277344,33.1373252868652,30.7469062805176,28.5165481567383,26.9057102203369,25.0044822692871,23.2345237731934,20.8397541046143,19.2261028289795,17.8055305480957,16.3429832458496,15.173300743103,13.3189630508423,12.1194944381714,11.6675472259521,22.9568252563477,61.9389266967773,54.2313270568848,16.8328342437744,7.14372968673706,6.36283874511719,5.68834257125854,5.20053243637085,4.70265054702759,4.49306154251099
292.029998779297,12.5515785217285,15.2342157363892,17.860668182373,20.7128601074219,24.3374519348145,27.5379524230957,31.0039157867432,34.2450523376465,36.4704704284668,40.5526542663574,43.319953918457,46.0796546936035,48.8112182617188,50.504524230957,51.8680000305176,52.7387886047363,52.4364356994629,52.8608703613281,52.6561698913574,52.7649803161621,52.4214401245117,52.9266395568848,52.6539840698242,51.4566917419434,50.7894897460937,49.0688552856445,47.0725212097168,44.8861274719238,42.5015525817871,40.313404083252,39.0502815246582,36.427318572998,34.2075347900391,31.843147277832,29.8690223693848,27.5666332244873,25.7452583312988,23.8300094604492,22.0810394287109,20.0860576629639,18.3934192657471,17.1226806640625,15.5786418914795,14.1440734863281,12.6415157318115,11.5818395614624,10.4505929946899,13.283164024353,48.3891334533691,58.9646949768066,29.2827930450439,8.54113674163818,5.85121726989746,5.40816020965576,4.68171501159668,4.27833843231201,3.89794135093689

From this output, we see that:

  1. The emission wavelengths are contained in the first column (250, 252, …).
  2. The excitation wavelengths are in the first row (50, 55, …). They are offsets to be applied to each excitation. For examples:
    • The emissions at excitation 250 nm are 250 + 50, 250 + 55, 250 + 60, …
    • The emissions at excitation 252 nm are 252 + 50, 252 + 55, 252 + 60, …
  3. The fluorescence data start at row 3 and column 2.

The first thing we need to do is to create a function that will read this data in a format that can be used by eemR. The function needs to meet these flowing criteria:

  1. Have an argument file that will contains the path of the file(s) to read.
  2. Return a list containing the flowing elements:
    • file: the path of the file
    • em: a numeric vector containing emission wavelengths.
    • ex: a numeric vector containing excitation wavelengths.
    • x: a matrix of length(em) rows by length(ex) columns.

Further more, the x matrix of the list need to be arranged as follow:

Let’s now write a function that will read the eem file and format the data accordingly. In this particular example, fluorescence has been measured in asynchronous mode. Hence, extra manipulations are needed to get the data on a regular grid.


library(dplyr)
library(tidyr)
library(eemR)

import_cary <- function(file) {
  dat <- read.csv(file, nrows = 102, skip = 1)

  ex <- na.omit(dat[, 1])
  em <- seq(50, 330, by = 5)

  em <- outer(ex, em, "+")
  em <- as.vector(em)
  ex <- rep(ex, 57)

  x <- dat[, -1]
  x <- x[-1, ]
  x <- matrix(as.numeric(unlist(x, use.names = FALSE)), ncol = 101, byrow = FALSE)

  res <- tibble(ex, em, x = as.vector(x)) %>%
    arrange(ex, em) %>%
    complete(ex, em, fill = list(x = NA))

  ex <- sort(unique(ex))
  em <- sort(unique(em))
  x <- matrix(res$x, ncol = length(ex), byrow = TRUE)

  # We need to interpolate because you do not have a regular grid (i.e. asynchronous)
  r <- MBA::mba.surf(res %>% drop_na(), no.X = 200, no.Y = 200, extend = FALSE)

  l <- list(
    file = file,
    x = t(r$xyz.est$z),
    ex = r$xyz.est$x,
    em = r$xyz.est$y
  )

  return(l)
}

We can now try our function and have a look to the structure of the returned list.

We will use the import_function argument of the eem_read() function to tell eemR how to read our file.

We can visualize the eem by using the plot() function:

plot(eem)

All other functions of the eemR package can now be used on the created eem. For example, we can remove the second order scattering.