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library(mascarade)
library(data.table)
library(ggplot2)
library(ggsci)example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/pbmc3k_umap.rds"))
data <- data.table(example$dims,
cluster=example$clusters)
maskTable <- generateMask(dims=example$dims,
clusters=example$clusters)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=cluster)) +
geom_path(data=maskTable, aes(group=group)) +
coord_fixed() +
theme_classic()
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/pbmc3k_tsne.rds"))
data <- data.table(example$dims,
cluster=example$clusters)
maskTable <- generateMask(dims=example$dims,
clusters=example$clusters)
ggplot(data, aes(x=tSNE_1, y=tSNE_2)) +
geom_point(aes(color=cluster)) +
geom_path(data=maskTable, aes(group=group)) +
coord_fixed() +
theme_classic()
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/aya.rds"))
data <- data.table(example$dims,
cluster=example$clusters)
maskTable <- generateMask(dims=example$dims,
clusters=example$clusters)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=cluster), size=0.5) +
geom_path(data=maskTable, aes(group=group)) +
coord_fixed() +
theme_classic()
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/chiajung1.rds"))
data <- data.table(example$dims,
cluster=example$clusters)
maskTable <- generateMask(dims=example$dims,
clusters=example$clusters)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=cluster), size=0.1) +
scale_color_ucscgb() +
geom_path(data=maskTable, aes(group=group)) +
coord_fixed() +
theme_classic()
example <- readRDS(url("https://alserglab.wustl.edu/files/mascarade/examples/chiajung2.rds"))
data <- data.table(example$dims,
cluster=example$clusters)
maskTable <- generateMask(dims=example$dims,
clusters=example$clusters)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=cluster)) +
geom_path(data=maskTable, aes(group=group)) +
coord_fixed() +
theme_classic()
sessionInfo()## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Debian GNU/Linux 13 (trixie)
##
## 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-r0.3.21.so; LAPACK version 3.11.0
##
## locale:
## [1] LC_CTYPE=C.utf8 LC_NUMERIC=C LC_TIME=C.utf8
## [4] LC_COLLATE=C LC_MONETARY=C.utf8 LC_MESSAGES=C.utf8
## [7] LC_PAPER=C.utf8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.utf8 LC_IDENTIFICATION=C
##
## time zone: US/Central
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggsci_4.2.0 ggplot2_4.0.1 data.table_1.18.0 mascarade_0.3.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.10 generics_0.1.4 spatstat.explore_3.6-0
## [4] tensor_1.5.1 spatstat.data_3.1-9 lattice_0.22-7
## [7] digest_0.6.39 magrittr_2.0.4 spatstat.utils_3.2-0
## [10] evaluate_1.0.5 grid_4.5.1 RColorBrewer_1.1-3
## [13] fastmap_1.2.0 jsonlite_2.0.0 Matrix_1.7-4
## [16] spatstat.sparse_3.1-0 scales_1.4.0 tweenr_2.0.3
## [19] jquerylib_0.1.4 abind_1.4-8 cli_3.6.5
## [22] rlang_1.1.6 polyclip_1.10-7 withr_3.0.2
## [25] cachem_1.1.0 yaml_2.3.12 otel_0.2.0
## [28] spatstat.univar_3.1-5 tools_4.5.1 deldir_2.0-4
## [31] dplyr_1.1.4 spatstat.geom_3.6-1 vctrs_0.6.5
## [34] R6_2.6.1 lifecycle_1.0.4 MASS_7.3-65
## [37] pkgconfig_2.0.3 pillar_1.11.1 bslib_0.9.0
## [40] gtable_0.3.6 glue_1.8.0 ggforce_0.5.0
## [43] xfun_0.55 tibble_3.3.0 tidyselect_1.2.1
## [46] knitr_1.51 goftest_1.2-3 farver_2.1.2
## [49] htmltools_0.5.9 spatstat.random_3.4-3 nlme_3.1-168
## [52] labeling_0.4.3 rmarkdown_2.30 compiler_4.5.1
## [55] S7_0.2.1These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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