NanoSIMS data processing of LANS data in R

This R markdown example demonstrates the basic functionality of the lans2r package.

Load data

To load data into R, export it from LANS which creates a folder for each analysis with sub folders dat containing the aggregated information about the different ROIs (in text file format) and mat containing the raw ion maps (in Matlab file format). Both of these can be imported easily with this package. For easier demonstration lans2r bundles a set of 3 analyses (folders analysis1, analysis2 and analysis3) with the package sources.

library(lans2r)
library(dplyr)
library(knitr)
folder <- system.file("extdata", "nanosims_data", package = "lans2r") # data base directory

ROI overview data

This loads the ROI overview data for the 3 analyses and assigns some additional information to the analyses (here rather random, column info). Since the parameters quiet=F indicates that information messages should be provided, it also outputs a summary of the loaded data.

## INFO: folder 'analysis1' read successfully.
##       Data for 37 ROIs with 4 ions recovered: 12C, 13C, 14N12C, 15N12C.
##       Z-stacks were loaded. Recovered 2 planes.
## INFO: folder 'analysis2' read successfully.
##       Data for 33 ROIs with 4 ions recovered: 12C, 13C, 14N12C, 15N12C.
##       Z-stacks were loaded. Recovered 2 planes.
## INFO: folder 'analysis3' read successfully.
##       Data for 34 ROIs with 4 ions recovered: 12C, 13C, 14N12C, 15N12C.
##       Z-stacks were loaded. Recovered 2 planes.

To calculate ratios and abundances, simply specify which ions you would like to ratio. Note: for convenience, we make use of the pipe operator %>% for chaining multiple operations. For more information on the pipe, take a look at the magrittr package.

## INFO: 624 'ion_sum' values + errors calculated, 624 added (subset: all)
##       values added (stored in 'variable' column): '13C+12C' (312x), '15N12C+14N12C' (312x)
## INFO: 936 'ratio' values + errors calculated, 936 added (subset: all)
##       values added (stored in 'variable' column): '13C+12C/15N12C+14N12C' (312x), '13C/12C' (312x), '15N12C/14N12C' (312x)
## INFO: 624 'abundance' values + errors calculated, 624 added (subset: all)
##       values added (stored in 'variable' column): '13C F' (312x), '15N12C F' (312x)

For additional operations, one can use the more generic calculate function and provide custom functions for value and error calculations and name construction. Here, we have APE (atom percent enrichment) as an example. For additional examples on calculate, see the vignette("lans2r-calculate").

## INFO: 624 'APE' values + errors calculated, 624 added (subset: all)
##       values added (stored in 'variable' column): '13C APE [%]' (312x), '15N12C APE [%]' (312x)

Overview

Let’s take a look at the first couple of rows of the data frame.

analysis info plane ROI data_type variable value sigma coord_x coord_y size pixels LW_ratio F13C_natural F15N_natural
analysis1 turtle all 1 ion_count 12C 1895850 1376.89869 17.38 192.93 0.83 353 2.45 0.0111 0.00366
analysis1 turtle all 2 ion_count 12C 1273919 1128.68020 18.39 175.25 0.75 290 1.57 0.0111 0.00366
analysis1 turtle all 3 ion_count 12C 1315417 1146.91630 40.38 168.26 0.70 250 1.66 0.0111 0.00366
analysis1 turtle all 4 ion_count 12C 1289955 1135.76186 42.05 207.80 0.72 267 2.16 0.0111 0.00366
analysis1 turtle all 5 ion_count 12C 1756159 1325.20149 42.92 147.66 0.81 334 2.50 0.0111 0.00366
analysis1 turtle all 6 ion_count 12C 1023934 1011.89624 46.56 103.93 0.67 232 2.11 0.0111 0.00366
analysis1 turtle all 7 ion_count 12C 5509 74.22264 52.29 22.77 1.32 893 1.09 0.0111 0.00366
analysis1 turtle all 8 ion_count 12C 1117870 1057.29372 61.77 120.06 0.62 195 2.39 0.0111 0.00366
analysis1 turtle all 9 ion_count 12C 1122839 1059.64098 63.38 146.02 0.65 217 2.02 0.0111 0.00366
analysis1 turtle all 10 ion_count 12C 1046665 1023.06647 74.39 98.29 0.66 221 2.23 0.0111 0.00366

Since this is now in long format so it’s easy to have both value and the sigma error, it’s hard to see line by line what is going on, let’s look just at analysis1 and recast the values into a wide format using the spread_data function.

analysis info plane ROI coord_x coord_y size pixels LW_ratio F13C_natural F15N_natural 12C 13C 13C APE [%] 13C F 13C+12C 13C+12C/15N12C+14N12C 13C/12C 14N12C 15N12C 15N12C APE [%] 15N12C F 15N12C+14N12C 15N12C/14N12C 12C sigma 13C APE [%] sigma 13C F sigma 13C sigma 13C+12C sigma 13C+12C/15N12C+14N12C sigma 13C/12C sigma 14N12C sigma 15N12C APE [%] sigma 15N12C F sigma 15N12C sigma 15N12C+14N12C sigma 15N12C/14N12C sigma
analysis1 turtle all 1 17.38 192.93 0.83 353 2.45 0.0111 0.00366 1895850 24315 0.1562974 0.0126630 1920165 0.2413707 0.0128254 7839685 115568 1.0867256 0.0145273 7955253 0.0147414 1376.89869 0.0080692 0.0000807 155.932678 1385.70018 0.0001941 0.0000828 2799.9437 0.0042422 0.0000424 339.95294 2820.5058 0.0000437
analysis1 turtle all 2 18.39 175.25 0.75 290 1.57 0.0111 0.00366 1273919 16087 0.1370485 0.0124705 1290006 0.2259213 0.0126280 5625982 83997 1.1050562 0.0147106 5709979 0.0149302 1128.68020 0.0097706 0.0000977 126.834538 1135.78431 0.0002202 0.0001002 2371.9153 0.0050382 0.0000504 289.82236 2389.5562 0.0000519
analysis1 turtle all 3 40.38 168.26 0.70 250 1.66 0.0111 0.00366 1315417 17084 0.1721004 0.0128210 1332501 0.2262195 0.0129875 5802914 87388 1.1175912 0.0148359 5890302 0.0150593 1146.91630 0.0097460 0.0000975 130.705777 1154.34007 0.0002170 0.0001000 2408.9238 0.0049813 0.0000498 295.61461 2426.9944 0.0000513
analysis1 turtle all 4 42.05 207.80 0.72 267 2.16 0.0111 0.00366 1289955 16221 0.1318694 0.0124187 1306176 0.2229323 0.0125749 5773380 85690 1.0965188 0.0146252 5859070 0.0148423 1135.76186 0.0096900 0.0000969 127.361690 1142.88057 0.0002157 0.0000994 2402.7859 0.0049595 0.0000496 292.72854 2420.5516 0.0000511
analysis1 turtle all 5 42.92 147.66 0.81 334 2.50 0.0111 0.00366 1756159 22267 0.1420622 0.0125206 1778426 0.2427387 0.0126794 7218762 107741 1.1045652 0.0147057 7326503 0.0149251 1325.20149 0.0083379 0.0000834 149.221312 1333.57639 0.0002029 0.0000855 2686.7754 0.0044471 0.0000445 328.23924 2706.7514 0.0000458
analysis1 turtle all 6 46.56 103.93 0.67 232 2.11 0.0111 0.00366 1023934 13166 0.1595015 0.0126950 1037100 0.2303558 0.0128583 4434979 67186 1.1263043 0.0149230 4502165 0.0151491 1011.89624 0.0109934 0.0001099 114.743191 1018.38107 0.0002509 0.0001128 2105.9390 0.0057142 0.0000571 259.20262 2121.8306 0.0000589
analysis1 turtle all 7 52.29 22.77 1.32 893 1.09 0.0111 0.00366 5509 75 0.2331232 0.0134312 5584 0.1079555 0.0136141 51019 706 0.9989106 0.0136491 51725 0.0138380 74.22264 0.1540455 0.0015405 8.660254 74.72617 0.0015207 0.0015827 225.8739 0.0510173 0.0005102 26.57066 227.4313 0.0005244
analysis1 turtle all 8 61.77 120.06 0.62 195 2.39 0.0111 0.00366 1117870 13971 0.1243607 0.0123436 1131841 0.2294823 0.0124979 4858391 73758 1.1294536 0.0149545 4932149 0.0151816 1057.29372 0.0103784 0.0001038 118.198985 1063.88016 0.0002392 0.0001064 2204.1758 0.0054651 0.0000547 271.58424 2220.8442 0.0000563
analysis1 turtle all 9 63.38 146.02 0.65 217 2.02 0.0111 0.00366 1122839 14201 0.1389446 0.0124894 1137040 0.2325619 0.0126474 4818643 70550 1.0769784 0.0144298 4889193 0.0146411 1059.64098 0.0104149 0.0001041 119.167949 1066.32078 0.0002421 0.0001068 2195.1408 0.0053933 0.0000539 265.61250 2211.1520 0.0000555
analysis1 turtle all 10 74.39 98.29 0.66 221 2.23 0.0111 0.00366 1046665 13408 0.1548186 0.0126482 1060073 0.2328937 0.0128102 4484536 67210 1.1105762 0.0147658 4551746 0.0149871 1023.06647 0.0108538 0.0001085 115.792919 1029.59847 0.0002512 0.0001113 2117.6723 0.0056534 0.0000565 259.24892 2133.4821 0.0000582

Or for more specific overviews, for example, only the abundance and APE, only the data values (excluding the errors) and only the first plane of the first few ROIs

analysis info plane ROI coord_x coord_y size pixels LW_ratio F13C_natural F15N_natural 13C APE [%] 13C F 15N12C APE [%] 15N12C F
analysis1 turtle 1 1 17.38 192.93 0.83 353 2.45 0.0111 0.00366 0.1645876 0.0127459 1.058593 0.0142459
analysis1 turtle 1 2 18.39 175.25 0.75 290 1.57 0.0111 0.00366 0.1446352 0.0125464 1.090331 0.0145633
analysis1 turtle 1 3 40.38 168.26 0.70 250 1.66 0.0111 0.00366 0.1711441 0.0128114 1.092983 0.0145898
analysis2 jetpack 1 1 25.28 128.10 1.38 976 1.04 0.0111 0.00366 0.2299359 0.0133994 2.633973 0.0299997
analysis2 jetpack 1 2 28.10 203.98 0.66 221 2.29 0.0111 0.00366 0.5019285 0.0161193 3.283767 0.0364977
analysis2 jetpack 1 3 40.89 21.97 0.66 225 1.73 0.0111 0.00366 0.4311799 0.0154118 3.361709 0.0372771
analysis3 pizza 1 1 31.42 209.93 0.82 348 3.32 0.0111 0.00366 0.4568719 0.0156687 3.324170 0.0369017
analysis3 pizza 1 2 32.36 37.12 0.73 276 1.89 0.0111 0.00366 0.2947689 0.0140477 3.316543 0.0368254
analysis3 pizza 1 3 40.78 151.29 1.50 1158 1.55 0.0111 0.00366 0.0854406 0.0119544 2.731920 0.0309792

Ion maps

Again, loading the ion maps for all 3 analyses.

## INFO: folder 'analysis1' read successfully.
##       Ion map data for 256 x 256 pixel frame (10.014 microm^2) for 4 ions recovered: 12C, 13C, 14N12C, 15N12C.
##       37 ROIs identified in the frame.
## INFO: folder 'analysis2' read successfully.
##       Ion map data for 256 x 256 pixel frame (10.014 microm^2) for 4 ions recovered: 12C, 13C, 14N12C, 15N12C.
##       33 ROIs identified in the frame.
## INFO: folder 'analysis3' read successfully.
##       Ion map data for 256 x 256 pixel frame (10.014 microm^2) for 4 ions recovered: 12C, 13C, 14N12C, 15N12C.
##       34 ROIs identified in the frame.

The data in these looks similar to the summary data frame except that it is broken out pixel by pixel:

analysis x.px y.px frame_size.px x.um y.um frame_size.um variable data_type value sigma ROI
analysis1 1 1 256 0.0391172 0.0391172 10.014 12C ion_count 1721 41.48494 0
analysis1 1 2 256 0.0391172 0.0782344 10.014 12C ion_count 1694 41.15823 0
analysis1 1 3 256 0.0391172 0.1173516 10.014 12C ion_count 1508 38.83298 0
analysis1 1 4 256 0.0391172 0.1564688 10.014 12C ion_count 1297 36.01389 0
analysis1 1 5 256 0.0391172 0.1955859 10.014 12C ion_count 1136 33.70460 0
analysis1 1 6 256 0.0391172 0.2347031 10.014 12C ion_count 786 28.03569 0
analysis1 1 7 256 0.0391172 0.2738203 10.014 12C ion_count 702 26.49528 0
analysis1 1 8 256 0.0391172 0.3129375 10.014 12C ion_count 453 21.28380 0
analysis1 1 9 256 0.0391172 0.3520547 10.014 12C ion_count 319 17.86057 0
analysis1 1 10 256 0.0391172 0.3911719 10.014 12C ion_count 220 14.83240 0

To make it easier to plot these kind of maps, lans2r provides a convenience function plot_maps but of course this could be adjusted as needed (look at the source code to see how this one is made). By default ion counts are normalized for each ion so they can be visualized on the same scale.