Comments (3)
andrewwbutler
commented on June 4, 2024
1
No problem. Happy to help out if there's anything else we can clarify or needs to be updated on the seurat-wrappers end to better integrate with the latest conos.
from seurat-data.
andrewwbutler
commented on June 4, 2024
Hi Evan,
We don't actively support v2 anymore and would recommend just updating the Seurat objects to the latest version using UpdateSeuratObject. For v4 objects, there is very little in terms of the object structure that changed but similarly, you should be able to run UpdateSeuratObject on any of the v3 objects there. You can find some documentation on the object structure here.
As far as the seurat-wrappers example, can you clarify the cases where it works and doesn't work? It looks like that vignette was last built July 2019 (probably corresponding to conos v.1.2.0) so it's possible that updates to either conos or Seurat could have affected it since. However, here's a reprex that seems to work for me using the latest Seurat v4.
library(Seurat)
#> Attaching SeuratObject
suppressWarnings(library(SeuratData))
#> Registered S3 method overwritten by 'cli':
#> method from
#> print.boxx spatstat.geom
#> ── Installed datasets ───────────────────────────────────── SeuratData v0.2.1 ──
#> ✓ ifnb 3.1.0 ✓ pbmc3k 3.1.4
#> ✓ panc8 3.0.2 ✓ stxBrain 0.1.1
#> ────────────────────────────────────── Key ─────────────────────────────────────
#> ✓ Dataset loaded successfully
#> > Dataset built with a newer version of Seurat than installed
#> ❓ Unknown version of Seurat installed
library(SeuratWrappers)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(conos)
#> Loading required package: Matrix
#> Loading required package: igraph
#>
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:dplyr':
#>
#> as_data_frame, groups, union
#> The following objects are masked from 'package:stats':
#>
#> decompose, spectrum
#> The following object is masked from 'package:base':
#>
#> union
data("ifnb")
ifnb.panel <- SplitObject(ifnb, split.by = "stim")
for (i in 1:length(ifnb.panel)) {
ifnb.panel[[i]] <- NormalizeData(ifnb.panel[[i]]) %>% FindVariableFeatures() %>% ScaleData() %>%
RunPCA(verbose = FALSE)
}
#> Centering and scaling data matrix
#> Centering and scaling data matrix
ifnb.con <- Conos$new(ifnb.panel)
ifnb.con$buildGraph(k = 15, k.self = 5, space = "PCA", ncomps = 30, n.odgenes = 2000, matching.method = "mNN",
metric = "angular", score.component.variance = TRUE, verbose = TRUE)
#> found 0 out of 1 cached PCA space pairs ...
#> running 1 additional PCA space pairs
#> Warning in scaledMatricesSeuratV3(so.objs = samples, data.type = data.type, :
#> Seurat doesn't support variance scaling
#> .
#> done
#> inter-sample links using mNN
#> Warning in scaledMatricesSeuratV3(so.objs = samples, data.type = data.type, :
#> Seurat doesn't support variance scaling
#> .
#> done
#> local pairs
#> done
#> building graph .
#> .
#> done
ifnb.con$findCommunities()
ifnb.con$embedGraph()
#> Estimating embeddings.
ifnb <- as.Seurat(ifnb.con)
#> Merging 2 samples
#> Adding pairwise alignments to 'conos.pairs' in miscellaneous data
#> Adding graph as 'RNA_mnn'
#> Warning: Adding a Graph without an assay associated with it
#> Adding graph embedding as largeVis
#> Adding clustering information
DimPlot(ifnb, reduction = "largeVis", group.by = c("stim", "ident", "seurat_annotations"), ncol = 3)
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
#>
#> 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
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] conos_1.4.1 igraph_1.2.6
#> [3] Matrix_1.3-4 dplyr_1.0.6
#> [5] SeuratWrappers_0.3.0 stxBrain.SeuratData_0.1.1
#> [7] pbmc3k.SeuratData_3.1.4 panc8.SeuratData_3.0.2
#> [9] ifnb.SeuratData_3.1.0 SeuratData_0.2.1
#> [11] SeuratObject_4.0.2 Seurat_4.0.3
#>
#> loaded via a namespace (and not attached):
#> [1] N2R_0.1.1 circlize_0.4.12 backports_1.2.1
#> [4] plyr_1.8.6 lazyeval_0.2.2 splines_4.1.0
#> [7] listenv_0.8.0 scattermore_0.7 ggplot2_3.3.4
#> [10] digest_0.6.27 foreach_1.5.1 htmltools_0.5.1.1
#> [13] fansi_0.5.0 magrittr_2.0.1 tensor_1.5
#> [16] cluster_2.1.2 doParallel_1.0.16 ROCR_1.0-11
#> [19] remotes_2.3.0 ComplexHeatmap_2.8.0 globals_0.14.0
#> [22] matrixStats_0.59.0 spatstat.sparse_2.0-0 sccore_0.1.3
#> [25] colorspace_2.0-1 rappdirs_0.3.3 ggrepel_0.9.1
#> [28] xfun_0.24 crayon_1.4.1 jsonlite_1.7.2
#> [31] spatstat.data_2.1-0 survival_3.2-11 zoo_1.8-9
#> [34] iterators_1.0.13 glue_1.4.2 polyclip_1.10-0
#> [37] gtable_0.3.0 leiden_0.3.8 GetoptLong_1.0.5
#> [40] leidenAlg_0.1.1 shape_1.4.6 future.apply_1.7.0
#> [43] BiocGenerics_0.38.0 abind_1.4-5 scales_1.1.1
#> [46] DBI_1.1.1 miniUI_0.1.1.1 Rcpp_1.0.6
#> [49] viridisLite_0.4.0 xtable_1.8-4 clue_0.3-59
#> [52] reticulate_1.20 spatstat.core_2.1-2 rsvd_1.0.5
#> [55] stats4_4.1.0 htmlwidgets_1.5.3 httr_1.4.2
#> [58] RColorBrewer_1.1-2 ellipsis_0.3.2 ica_1.0-2
#> [61] farver_2.1.0 pkgconfig_2.0.3 uwot_0.1.10
#> [64] deldir_0.2-10 utf8_1.2.1 labeling_0.4.2
#> [67] tidyselect_1.1.1 rlang_0.4.11 reshape2_1.4.4
#> [70] later_1.2.0 pbmcapply_1.5.0 munsell_0.5.0
#> [73] tools_4.1.0 cli_2.5.0 generics_0.1.0
#> [76] ggridges_0.5.3 evaluate_0.14 stringr_1.4.0
#> [79] fastmap_1.1.0 yaml_2.2.1 goftest_1.2-2
#> [82] knitr_1.33 fs_1.5.0 fitdistrplus_1.1-5
#> [85] purrr_0.3.4 RANN_2.6.1 pbapply_1.4-3
#> [88] future_1.21.0 nlme_3.1-152 mime_0.10
#> [91] grr_0.9.5 compiler_4.1.0 rstudioapi_0.13
#> [94] plotly_4.9.3 png_0.1-7 spatstat.utils_2.1-0
#> [97] reprex_2.0.0 tibble_3.1.2 stringi_1.6.2
#> [100] highr_0.9 lattice_0.20-44 styler_1.4.1
#> [103] vctrs_0.3.8 pillar_1.6.1 lifecycle_1.0.0
#> [106] BiocManager_1.30.16 GlobalOptions_0.1.2 spatstat.geom_2.1-0
#> [109] lmtest_0.9-38 RcppAnnoy_0.0.18 data.table_1.14.0
#> [112] cowplot_1.1.1 irlba_2.3.3 Matrix.utils_0.9.8
#> [115] httpuv_1.6.1 patchwork_1.1.1 R6_2.5.0
#> [118] promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3
#> [121] IRanges_2.26.0 parallelly_1.25.0 codetools_0.2-18
#> [124] MASS_7.3-54 assertthat_0.2.1 rjson_0.2.20
#> [127] withr_2.4.2 sctransform_0.3.2 S4Vectors_0.30.0
#> [130] mgcv_1.8-36 parallel_4.1.0 grid_4.1.0
#> [133] rpart_4.1-15 tidyr_1.1.3 rmarkdown_2.8
#> [136] Cairo_1.5-12.2 Rtsne_0.15 shiny_1.6.0Created on 2021-06-17 by the reprex package (v2.0.0)
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evanbiederstedt
commented on June 4, 2024
Thanks for the help!
We don't actively support v2 anymore and would recommend just updating the Seurat objects to the latest version using UpdateSeuratObject. For v4 objects, there is very little in terms of the object structure that changed but similarly, you should be able to run UpdateSeuratObject on any of the v3 objects there. You can find some documentation on the object structure here.
Thanks! After digging around, I think I understand the Seurat classes a bit better now---there's a version field we can access.
Here is version 2: https://github.com/satijalab/seurat/blob/65b77a9480281ef9ab1aa8816f7c781752092c18/R/seurat.R#L8-L71
seurat <- setClass(
"seurat",
slots = c(
raw.data = "ANY",
data = "ANY",
scale.data = "ANY",
var.genes = "vector",
is.expr = "numeric",
ident = "factor",
meta.data = "data.frame",
project.name = "character",
dr = "list",
assay = "list",
hvg.info = "data.frame",
imputed = "data.frame",
cell.names = "vector",
cluster.tree = "list",
snn = "dgCMatrix",
calc.params = "list",
kmeans = "ANY",
spatial = "ANY",
misc = "ANY",
version = "ANY"
)
)
The changelog then details the modifications with v3: https://satijalab.org/seurat/news/index.html#seurat-3-0-0-2019-04-16-2019-04-15 (We've been looking around for details of the v3 -> v4 changes)
Here's the v3 class: https://github.com/satijalab/seurat/blob/25b830b0dd6f12538516f0faf9a3b3ddfd0ce6d8/R/objects.R#L237
Seurat <- setClass(
Class = 'Seurat',
slots = c(
assays = 'list',
meta.data = 'data.frame',
active.assay = 'character',
active.ident = 'factor',
graphs = 'list',
neighbors = 'list',
reductions = 'list',
project.name = 'character',
misc = 'list',
version = 'package_version',
commands = 'list',
tools = 'list'
)
)
You can find some documentation on the object structure here.
Ah, so this page refers to v3 and v4: https://github.com/satijalab/seurat/wiki/Seurat#slots
That clarifies things, thank you
RE: UpdateSeuratObject()
I guess one could argue that this function should be run on all *rds "Seurat" object given...
As far as the seurat-wrappers example, can you clarify the cases where it works and doesn't work? It looks like that vignette was last built July 2019 (probably corresponding to conos v.1.2.0) so it's possible that updates to either conos or Seurat could have affected it since. However, here's a reprex that seems to work for me using the latest Seurat v4.
This also clarifies some internal confusion on our end. You're using the latest version of conos....and Seurat v4. I'll track down precisely what is going on and update kharchenkolab/conos#101
I appreciate the help here!
Best, Evan
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