error in createGiottoCosMxObject() at Joining FOV gobjects

[drosop]

Hi,

Im trying to test Nanonstring CosMx Lung tutorial (https://giottosuite.readthedocs.io/en/latest/subsections/datasets/Nanostring_Lung12.html#cosmx-project-loading-function).
However, Im stuck at createGiottoCosMxObject() step.

Error:
Error in setSpatialLocations(gobject = gobject, x = x, ...) :
Add expression or spatial (polygon) information first

I'm following exactly the same steps as in tutorial. Test creating giotto object for individual fovs and then joining them (steps 2-4). But encountering same problem at joinGiottoObjects().

Can you please help?

Thank you,

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 8.7 (Ootpa)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.15.so; LAPACK version 3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Chicago
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Giotto_4.1.0 GiottoClass_0.3.5

loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 tidyr_1.3.1 plotly_4.10.4
[4] utf8_1.2.4 generics_0.1.3 gtools_3.9.5
[7] stringi_1.8.4 lattice_0.22-6 digest_0.6.37
[10] magrittr_2.0.3 grid_4.4.1 RColorBrewer_1.1-3
[13] fastmap_1.2.0 plyr_1.8.9 R.oo_1.26.0
[16] jsonlite_1.8.8 Matrix_1.7-0 R.utils_2.12.3
[19] ggrepel_0.9.6 backports_1.5.0 scattermore_1.2
[22] httr_1.4.7 purrr_1.0.2 fansi_1.0.6
[25] viridisLite_0.4.2 scales_1.3.0 lazyeval_0.2.2
[28] codetools_0.2-20 cli_3.6.3 rlang_1.1.4
[31] R.methodsS3_1.8.2 pak_0.8.0 cowplot_1.1.3
[34] munsell_0.5.1 withr_3.0.1 remotes_2.5.0
[37] colorRamp2_0.1.0 parallel_4.4.1 tools_4.4.1
[40] reshape2_1.4.4 deldir_2.0-4 GiottoUtils_0.1.11
[43] checkmate_2.3.2 dplyr_1.1.4 colorspace_2.1-1
[46] ggplot2_3.5.1 curl_5.2.2 reticulate_1.39.0
[49] vctrs_0.6.5 R6_2.5.1 png_0.1-8
[52] matrixStats_1.4.1 lifecycle_1.0.4 magick_2.8.4
[55] stringr_1.5.1 htmlwidgets_1.6.4 GiottoVisuals_0.2.4
[58] dbscan_1.2-0 pkgconfig_2.0.3 terra_1.7-78
[61] pillar_1.9.0 gtable_0.3.5 data.table_1.16.0
[64] glue_1.7.0 Rcpp_1.0.13 tibble_3.2.1
[67] tidyselect_1.2.1 htmltools_0.5.8.1 igraph_2.0.3
[70] compiler_4.4.1 sp_2.1-4

[jiajic]

Hi @drosop,

Sorry for the issue. The load part of that tutorial is due an update. Can you try the following?

library(Giotto)
cosmx <- importCosMx("directory path to cosmx outputs")
g <- cosmx$create_gobject()

Further information on our updates to cosmx loading with Giotto can be found here

[drosop]

Thank you so much for quick response.

It is working now. However, I encounter few issues:

1. importCosMx() isnt automatically detecting fov position file and metadata file. So I wrote this:

data_path = '~/Lung12-Flat_files_and_images/'

cosmx <- importCosMx(cosmx_dir = data_path,
                     fovs = c(2,3,4))

fov_shifts <- data.table::fread(paste0(data_path,"/Lung12_fov_positions_file.csv"))
if (!"X_mm" %in% colnames(fov_shifts)) {
  data.table::setnames(fov_shifts, new = c("fov", "x", "y"))
  pos <- fov_shifts
}
cosmx$offsets <- pos

Can you please see if this is the right way?

2. When creating image using spatInSituPlotPoints(), the y dims look weird. Polygons and expression data is plotted separately. See attached. Can you please suggest why is this happening? Im following steps on : https://gist.github.com/jiajic/bc8abf18fd362ca36790b8c074847bb9#file-cosmx_importer-md

cosmx$create_gobject()

Warning messages:
1: In data.table::fread(input = path, nThread = cores, drop = dropcols) :
  Column name 'cell' (drop[4]) not found

test2.pdf

Thank you,

[rbutleriii]

FYI, came across while looking for something else, but https://giottosuite.readthedocs.io/ is the old website (even though it is the top search engine hit), you want drieslab.github.io. The issue is you need to run createGiottoCosMxObject() with the version = 'legacy' setting.