Last updated: 2024-04-14
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Knit directory: muse/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 72ffea9 | Dave Tang | 2024-04-14 | Getting started with harmony |
Follow the quickstart tutorial
install.packages("harmony")Load {harmony}.
library("harmony")Loading required package: RcpppackageVersion("harmony")[1] '1.2.0'We library normalized the cells, log transformed the counts, and scaled the genes. Then we performed PCA and kept the top 20 PCs. The PCA embeddings and meta data are available as part of this package.
data(cell_lines)
V <- cell_lines$scaled_pcs
meta_data <- cell_lines$meta_data
head(meta_data)# A tibble: 6 × 5
cell_id dataset nGene percent_mito cell_type
<chr> <chr> <int> <dbl> <chr>
1 half_GTACGAACCACCAA half 1508 0.0148 jurkat
2 t293_AGGTCATGCACTTT t293 4009 0.0232 t293
3 half_ATAGTTGACTTCTA half 3545 0.0153 jurkat
4 half_GAGCGGCTTGCTTT half 2450 0.0170 jurkat
5 jurkat_CTGATACTCCGTAA jurkat 2388 0.0601 jurkat
6 half_GTGGAGGACTGTTT half 3762 0.0211 t293 Initially, the cells cluster by both dataset (left) and cell type
(right). Can’t find the do_scatter function.
Let’s run Harmony to remove the influence of dataset-of-origin from the cell embeddings.
harmony_embeddings <- harmony::RunHarmony(
V, meta_data, 'dataset', verbose=FALSE
)
dim(harmony_embeddings)[1] 2370 20
sessionInfo()R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 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/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
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
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] harmony_1.2.0 Rcpp_1.0.12 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.9 utf8_1.2.4 generics_0.1.3
[4] lattice_0.22-5 stringi_1.8.3 digest_0.6.35
[7] magrittr_2.0.3 evaluate_0.23 grid_4.3.3
[10] fastmap_1.1.1 rprojroot_2.0.4 jsonlite_1.8.8
[13] Matrix_1.6-5 processx_3.8.4 whisker_0.4.1
[16] ps_1.7.6 promises_1.3.0 httr_1.4.7
[19] fansi_1.0.6 scales_1.3.0 RhpcBLASctl_0.23-42
[22] codetools_0.2-19 jquerylib_0.1.4 cli_3.6.2
[25] rlang_1.1.3 cowplot_1.1.3 munsell_0.5.1
[28] cachem_1.0.8 yaml_2.3.8 tools_4.3.3
[31] dplyr_1.1.4 colorspace_2.1-0 ggplot2_3.5.0
[34] httpuv_1.6.15 vctrs_0.6.5 R6_2.5.1
[37] lifecycle_1.0.4 git2r_0.33.0 stringr_1.5.1
[40] fs_1.6.3 pkgconfig_2.0.3 callr_3.7.6
[43] pillar_1.9.0 bslib_0.7.0 later_1.3.2
[46] gtable_0.3.4 glue_1.7.0 xfun_0.43
[49] tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.16.0
[52] knitr_1.46 htmltools_0.5.8.1 rmarkdown_2.26
[55] compiler_4.3.3 getPass_0.2-4