Clustered Dotplot about sccustomize HOT 9 CLOSED

It works now. Thanks!

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• Add unique check
• Solve bug #19 (*Issue with kmeansElbow Plot, see issue 19 for description)

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• Bug with setting color scale when using default values. See reprex in #19

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wasn't a bug in actual color scale on plot but in mix/max displayed in legend. Changed to new defaults for more consistent default results.

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Clustered_DotPlot function does not exist in the latest version of scCustomize that I have

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Hi @osmansharifi can you paste output of sessionInfo here?

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R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] scCustomize_0.7.0.0006 Seurat_4.1.0 viridis_0.6.2
[4] viridisLite_0.4.0 dplyr_1.0.8 reshape2_1.4.4
[7] ggplot2_3.3.5 SeuratObject_4.0.4

loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.24
[3] tidyselect_1.1.1 htmlwidgets_1.5.4
[5] grid_4.1.2 Rtsne_0.15
[7] devtools_2.4.3 munsell_0.5.0
[9] codetools_0.2-18 ica_1.0-2
[11] future_1.23.0 miniUI_0.1.1.1
[13] withr_2.4.3 colorspace_2.0-2
[15] Biobase_2.54.0 knitr_1.37
[17] rstudioapi_0.13 stats4_4.1.2
[19] SingleCellExperiment_1.16.0 ROCR_1.0-11
[21] ggsignif_0.6.3 tensor_1.5
[23] listenv_0.8.0 MatrixGenerics_1.6.0
[25] labeling_0.4.2 GenomeInfoDbData_1.2.7
[27] polyclip_1.10-0 farver_2.1.0
[29] pheatmap_1.0.12 rprojroot_2.0.2
[31] parallelly_1.30.0 vctrs_0.3.8
[33] generics_0.1.2 xfun_0.29
[35] dittoSeq_1.7.0 R6_2.5.1
[37] GenomeInfoDb_1.30.1 ggbeeswarm_0.6.0
[39] bitops_1.0-7 spatstat.utils_2.3-0
[41] cachem_1.0.6 DelayedArray_0.20.0
[43] assertthat_0.2.1 promises_1.2.0.1
[45] scales_1.1.1 beeswarm_0.4.0
[47] gtable_0.3.0 globals_0.14.0
[49] processx_3.5.2 goftest_1.2-3
[51] rlang_1.0.1 scatterplot3d_0.3-41
[53] splines_4.1.2 rstatix_0.7.0
[55] lazyeval_0.2.2 spatstat.geom_2.3-1
[57] broom_0.7.12 yaml_2.2.2
[59] abind_1.4-5 backports_1.4.1
[61] httpuv_1.6.5 usethis_2.1.5
[63] tools_4.1.2 ellipsis_0.3.2
[65] spatstat.core_2.3-2 RColorBrewer_1.1-2
[67] BiocGenerics_0.40.0 sessioninfo_1.2.2
[69] ggridges_0.5.3 Rcpp_1.0.8
[71] plyr_1.8.6 zlibbioc_1.40.0
[73] purrr_0.3.4 RCurl_1.98-1.6
[75] ps_1.6.0 prettyunits_1.1.1
[77] ggpubr_0.4.0 rpart_4.1.16
[79] deldir_1.0-6 pbapply_1.5-0
[81] cowplot_1.1.1 S4Vectors_0.32.3
[83] zoo_1.8-9 SummarizedExperiment_1.24.0
[85] ggrepel_0.9.1 cluster_2.1.2
[87] fs_1.5.2 magrittr_2.0.2
[89] RSpectra_0.16-0 data.table_1.14.2
[91] scattermore_0.7 lmtest_0.9-39
[93] RANN_2.6.1 fitdistrplus_1.1-6
[95] matrixStats_0.61.0 pkgload_1.2.4
[97] patchwork_1.1.1 mime_0.12
[99] evaluate_0.14 xtable_1.8-4
[101] IRanges_2.28.0 gridExtra_2.3
[103] testthat_3.1.2 compiler_4.1.2
[105] tibble_3.1.6 colorway_0.2.0
[107] KernSmooth_2.23-20 crayon_1.4.2
[109] htmltools_0.5.2 mgcv_1.8-38
[111] later_1.3.0 ggprism_1.0.3.9000
[113] tidyr_1.2.0 lubridate_1.8.0
[115] DBI_1.1.2 MASS_7.3-55
[117] Matrix_1.4-0 car_3.0-12
[119] brio_1.1.3 cli_3.1.1
[121] parallel_4.1.2 igraph_1.2.11
[123] GenomicRanges_1.46.1 forcats_0.5.1
[125] pkgconfig_2.0.3 plotly_4.10.0
[127] spatstat.sparse_2.1-0 paletteer_1.4.0
[129] vipor_0.4.5 XVector_0.34.0
[131] snakecase_0.11.0 stringr_1.4.0
[133] callr_3.7.0 digest_0.6.29
[135] sctransform_0.3.3 RcppAnnoy_0.0.19
[137] janitor_2.1.0 spatstat.data_2.1-2
[139] rmarkdown_2.11 leiden_0.3.9
[141] uwot_0.1.11 curl_4.3.2
[143] shiny_1.7.1 lifecycle_1.0.1
[145] nlme_3.1-155 jsonlite_1.7.3
[147] carData_3.0-5 desc_1.4.0
[149] limma_3.50.0 fansi_1.0.2
[151] pillar_1.7.0 lattice_0.20-45
[153] fastmap_1.1.0 httr_1.4.2
[155] pkgbuild_1.3.1 survival_3.2-13
[157] remotes_2.4.2 glue_1.6.1
[159] png_0.1-7 Polychrome_1.3.1
[161] stringi_1.7.6 rematch2_2.1.2
[163] memoise_2.0.1 irlba_2.3.5
[165] future.apply_1.8.1

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hmmm that's strange. I just ran fresh install off dev branch and works on my machine. I just pushed a new commit a minute ago to fix a typo in documentation of different function. I would try a redownload off dev branch and see if fresh install fixes it.

Code I ran

devtools::install_github("samuel-marsh/scCustomize", ref = "develop")

pbmc <- pbmc3k.SeuratData::pbmc3k.final

pbmc <- UpdateSeuratObject(pbmc)

Clustered_DotPlot(seurat_object = pbmc, features = c("PTPRC", "CD4", "CD14","CD19", "CD8A", "FCGR3A", "FCER1A"))

Best,
Sam

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Awesome!

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