Comments (6)
Makes sense to me. I used to just scramble the column order of the input SCE but I suppose that can be pretty expensive if you're not using DelayedArrays.
from scater.
Thanks Aaron,
For the scramble the column order of input SCE, you mean like below code?
example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce <- runPCA(example_sce, ncomponents=5)
plotUMAP(example_sce[, order(logcounts(example_sce["Gene_0001", ]))],
colour_by = "Gene_0001")
from scater.
Sounds good, thanks for raising the issue
from scater.
Hi
I find it seems that the order_by
parameter not work
library(scater)
example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce <- runPCA(example_sce)
example_sce <- runUMAP(example_sce)
plotUMAP(example_sce,
colour_by = "Gene_0001")
If I add order_by parameter, there is only some cells left
plotUMAP(example_sce,
colour_by = "Gene_0001",
order_by = "Gene_0001")
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Stream 8
Matrix products: default
BLAS: /opt/sysoft/R-4.2.0/lib64/R/lib/libRblas.so
LAPACK: /opt/sysoft/R-4.2.0/lib64/R/lib/libRlapack.so
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] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] scater_1.25.6 ggplot2_3.3.6
[3] scuttle_1.6.2 SingleCellExperiment_1.18.0
[5] SummarizedExperiment_1.26.1 Biobase_2.56.0
[7] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[9] IRanges_2.30.0 S4Vectors_0.34.0
[11] BiocGenerics_0.42.0 MatrixGenerics_1.8.0
[13] matrixStats_0.62.0
loaded via a namespace (and not attached):
[1] ggrepel_0.9.1 Rcpp_1.0.9 rsvd_1.0.5
[4] lattice_0.20-45 FNN_1.1.3.1 digest_0.6.29
[7] assertthat_0.2.1 utf8_1.2.2 RSpectra_0.16-1
[10] R6_2.5.1 pillar_1.7.0 sparseMatrixStats_1.8.0
[13] zlibbioc_1.42.0 rlang_1.0.3 rstudioapi_0.13
[16] irlba_2.3.5 Matrix_1.4-1 labeling_0.4.2
[19] BiocNeighbors_1.14.0 BiocParallel_1.30.2 RCurl_1.98-1.6
[22] munsell_0.5.0 uwot_0.1.11 beachmat_2.12.0
[25] DelayedArray_0.22.0 compiler_4.2.0 vipor_0.4.5
[28] BiocSingular_1.12.0 pkgconfig_2.0.3 ggbeeswarm_0.6.0
[31] tidyselect_1.1.2 tibble_3.1.7 gridExtra_2.3
[34] GenomeInfoDbData_1.2.8 fansi_1.0.3 viridisLite_0.4.0
[37] crayon_1.5.1 dplyr_1.0.9 withr_2.5.0
[40] bitops_1.0-7 grid_4.2.0 gtable_0.3.0
[43] lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.3
[46] scales_1.2.0 ScaledMatrix_1.4.0 cli_3.3.0
[49] farver_2.1.0 XVector_0.36.0 viridis_0.6.2
[52] DelayedMatrixStats_1.18.0 ellipsis_0.3.2 generics_0.1.2
[55] vctrs_0.4.1 cowplot_1.1.1 tools_4.2.0
[58] glue_1.6.2 beeswarm_0.4.0 purrr_0.3.4
[61] parallel_4.2.0 colorspace_2.0-3
from scater.
Ah yeah my bad, left out an order
when refactoring some code
from scater.
Thanks :), it work well now
from scater.
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from scater.