Error when using Fibroblast atlas for Symphony

[jk86754]

Hi Ilya,

I am trying to use the pre-built fibroblast atlas (https://sandbox.zenodo.org/record/772596#.YdRr5mDMIuV) in Symphony. I read in the RDS file as specified:

fibroblast_reference <- readRDS('fibroblast_atlas.rds')

When trying to plot the reference

p = plotReference(fibroblast_reference,
as.density = TRUE, # plot density or individual cells
bins = 14, # if density, nbins parameter for stat_density_2d
bandwidth = 1, # if density, bandwidth parameter for stat_density_2d
title = "Symphony Reference", # Plot title
color.by = 'Cluster', # metadata column name for cell type labels
show.legend = TRUE, # Show cell type legend
show.labels = TRUE, # Show cell type labels
show.centroids = FALSE) # Plot soft cluster centroid locations)

I get an error:

Error in plotReference(ref_pbmcs, as.density = TRUE, bins = 14, bandwidth = 1, :
Error: umap slot is empty. UMAP was not saved for this reference!

Any help would be appreciated!

sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

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

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

other attached packages:
[1] patchwork_1.1.1 RColorBrewer_1.1-2 ggrastr_1.0.1 ggthemes_4.2.4 plyr_1.8.6 Matrix_1.4-0 matrixStats_0.61.0 forcats_0.5.1
[9] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.1.1 tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
[17] singlecellmethods_0.1.0 data.table_1.14.2 symphony_0.1.0 harmony_0.1.0 Rcpp_1.0.7

loaded via a namespace (and not attached):
[1] fs_1.5.2 usethis_2.1.5 lubridate_1.8.0 devtools_2.4.3 httr_1.4.2 rprojroot_2.0.2 tools_4.0.4 backports_1.4.1 utf8_1.2.2 R6_2.5.1
[11] irlba_2.3.5 vipor_0.4.5 uwot_0.1.11 DBI_1.1.2 colorspace_2.0-2 withr_2.4.3 tidyselect_1.1.1 prettyunits_1.1.1 processx_3.5.2 curl_4.3.2
[21] compiler_4.0.4 cli_3.1.0 rvest_1.0.2 xml2_1.3.3 desc_1.4.0 scales_1.1.1 callr_3.7.0 pkgconfig_2.0.3 sessioninfo_1.2.2 dbplyr_2.1.1
[31] fastmap_1.1.0 rlang_0.4.12 readxl_1.3.1 rstudioapi_0.13 generics_0.1.1 jsonlite_1.7.2 magrittr_2.0.1 ggbeeswarm_0.6.0 munsell_0.5.0 fansi_0.5.0
[41] lifecycle_1.0.1 stringi_1.7.6 pkgbuild_1.3.1 grid_4.0.4 ggrepel_0.9.1 crayon_1.4.2 lattice_0.20-45 haven_2.4.3 cowplot_1.1.1 hms_1.1.1
[51] ps_1.6.0 pillar_1.6.4 codetools_0.2-18 pkgload_1.2.4 reprex_2.0.1 glue_1.6.0 remotes_2.4.2 modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0
[61] testthat_3.1.1 cellranger_1.1.0 gtable_0.3.0 RANN_2.6.1 assertthat_0.2.1 cachem_1.0.6 broom_0.7.11 beeswarm_0.4.0 memoise_2.0.1 ellipsis_0.3.2

If I understand your description correctly, I also need the uwot model file and the metadata. I may be just missing something but I am not sure how to find these in the R object you posted on zenodo.

I also posted this issue at immunogenomics/symphony#23

Thanks!