Hi There,
Im very impressed with this package, but am running into an issue as I am trying to read in our data.
Here is what the data look like:
> msa_pre
MSImagingArrays with 254387 spectra
spectraData(2): intensity, mz
pixelData(7): x, y, z, ..., 3DPositionX, 3DPositionY, 3DPositionZ
coord(3): x = 1...2002, y = 1...300, z = 1...1
runNames(1): tissue_fat_pad
experimentData(10): spectrumType, instrumentModel, ionSource, ..., scanType, lineScanDirection, pixelSize
centroided: NA
continuous: FALSE
And here is the coord slot:
> coord(msa_pre)
DataFrame with 254387 rows and 3 columns
x y z
<numeric> <numeric> <integer>
spectrum=0 57 124 1
spectrum=1 58 124 1
spectrum=2 59 124 1
spectrum=3 60 124 1
spectrum=4 61 124 1
... ... ... ...
spectrum=254382 357 233 1
spectrum=254383 358 233 1
spectrum=254384 359 233 1
spectrum=254385 360 233 1
spectrum=254386 361 233 1
I notice that x and y are numeric, and z is an integer.
When I try to plot by coord, I receive the following error:
> Cardinal::plot(msa_pre, coord = list(x = 57, y = 124, z = 1))
Error in plotlist[[1L]] : subscript out of bounds
In addition: Warning message:
in .find_positions(object, coord, run, tolerance): no match for coord x = 57, y = 124, z = 1; nearest is x = 57, y = 124, z = 1
I receive no such error when trying to plot by specifying the index:
> plot(msa_pre, i=2)
When I try to specify the type, I receive the same error:
> Cardinal::plot(msa_pre, coord = list(
+ x = as.numeric(57),
+ y = as.numeric(124),
+ z = as.integer(1)
+ ))
Error in plotlist[[1L]] : subscript out of bounds
In addition: Warning message:
in .find_positions(object, coord, run, tolerance): no match for coord x = 57, y = 124, z = 1; nearest is x = 57, y = 124, z = 1
I can see that the spectra exist at those coordinates:
> subset_spectrum <- spectra(msa_pre)[coord(msa_pre)$x == 57 & coord(msa_pre)$y == 124 & coord(msa_pre)$z == 1, ]
> str(subset_spectrum)
List of 1
$ spectrum=0: num [1:25511] 7 6 6 6 12 6 6 6 6 6 ...
Can you think of any reasons this could be? I note that there is only one z value, so removing that slot entirely would be a fine solution, if there are methods to achieve that.
Thank you very much,
Christian Potts
session info:
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.0.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[5] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[9] ggplot2_3.5.1 tidyverse_2.0.0 Cardinal_3.8.3 S4Vectors_0.44.0
[13] ProtGenerics_1.38.0 BiocGenerics_0.52.0 BiocParallel_1.40.0 BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] generics_0.1.3 tiff_0.1-12 renv_1.1.0 bitops_1.0-9 stringi_1.8.4
[6] jpeg_0.1-10 lattice_0.22-6 hms_1.1.3 digest_0.6.37 magrittr_2.0.3
[11] timechange_0.3.0 grid_4.4.1 fftwtools_0.9-11 fastmap_1.2.0 Matrix_1.7-1
[16] ontologyIndex_2.12 matter_2.8.0 scales_1.3.0 codetools_0.2-20 abind_1.4-8
[21] cli_3.6.3 rlang_1.1.5 CardinalIO_1.4.0 Biobase_2.66.0 EBImage_4.48.0
[26] munsell_0.5.1 withr_3.0.2 tools_4.4.1 parallel_4.4.1 tzdb_0.4.0
[31] colorspace_2.1-1 locfit_1.5-9.11 vctrs_0.6.5 R6_2.5.1 png_0.1-8
[36] lifecycle_1.0.4 htmlwidgets_1.6.4 irlba_2.3.5.1 pkgconfig_2.0.3 pillar_1.10.1
[41] gtable_0.3.6 glue_1.8.0 tidyselect_1.2.1 rstudioapi_0.17.1 htmltools_0.5.8.1
[46] nlme_3.1-166 compiler_4.4.1 RCurl_1.98-1.16
Hi There,
Im very impressed with this package, but am running into an issue as I am trying to read in our data.
Here is what the data look like:
And here is the coord slot:
I notice that x and y are numeric, and z is an integer.
When I try to plot by coord, I receive the following error:
I receive no such error when trying to plot by specifying the index:
> plot(msa_pre, i=2)When I try to specify the type, I receive the same error:
I can see that the spectra exist at those coordinates:
Can you think of any reasons this could be? I note that there is only one z value, so removing that slot entirely would be a fine solution, if there are methods to achieve that.
Thank you very much,
Christian Potts
session info: