can plotUMAP offer a order parameter

[shangguandong1996]

Hi, Dear Developer. I am wondering whehter plotUMAP or plotReducedDim can offer can option which can plot point according to the expression value like order parameter in FeaturePlot of Seurat. Because sometimes, my gene express in only some cells in one clusters. And it will be buried by others cell.

Best wishes

Guandong Shang

[LTLA]

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.

[shangguandong1996]

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")

[alanocallaghan]

Sounds good, thanks for raising the issue

[shangguandong1996]

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

[alanocallaghan]

Ah yeah my bad, left out an order when refactoring some code

[shangguandong1996]

Thanks :), it work well now