R source file which contains functions
- to run spatial clustering and markers finding for each sample. Thus easy to be applied on any samples
- to integrate samples and annotate the cell types
- to score any gene set spatially
Please clone the directory
testdata were found in testdata/
For utils 1.:
source("visiumR.r")
sample_ids <- list.dirs("testdata/", full.names = F, recursive = F)
lapply(sample_ids, run_single)
sessionInfo
$platform
$version
'R version 4.1.0 (2021-05-18)'
$os
'Ubuntu 20.04.6 LTS'
$system
'x86_64, linux-gnu'
$ui
'X11'
$language
'(EN)'
$collate
'en_US.UTF-8'
$ctype
'en_US.UTF-8'
$date
'2024-08-12'
$pandoc
'2.19.2'
$packages
A packages_info: 113 ร 11
package ondiskversion loadedversion path is_base date source md5ok
<chr> <chr> <chr> <chr> <lgl> <chr> <chr> <lgl>
abind abind 1.4.5 1.4-5 FALSE FALSE 2016-07-21 CRAN (R 4.1.3)
base64enc base64enc 0.1.3 0.1-3 FALSE FALSE 2015-07-28 CRAN (R 4.1.3)
bit bit 4.0.5 4.0.5 FALSE FALSE 2022-11-15 CRAN (R 4.1.3)
bit64 bit64 4.0.5 4.0.5 FALSE FALSE 2020-08-30 CRAN (R 4.1.3)
cli cli 3.6.1 3.6.1 FALSE FALSE 2023-03-23 CRAN (R 4.1.3)
cluster cluster 2.1.4 2.1.4 FALSE FALSE 2022-08-22 CRAN (R 4.1.3)
codetools codetools 0.2.19 0.2-19 FALSE FALSE 2023-02-01 CRAN (R 4.1.3)
colorspace colorspace 2.1.0 2.1-0 FALSE FALSE 2023-01-23 CRAN (R 4.1.3)
cowplot cowplot 1.1.1 1.1.1 TRUE FALSE 2020-12-30 CRAN (R 4.1.3)
crayon crayon 1.5.2 1.5.2 FALSE FALSE 2022-09-29 CRAN (R 4.1.3)
data.table data.table 1.14.8 1.14.8 FALSE FALSE 2023-02-17 CRAN (R 4.1.3)
deldir deldir 1.0.9 1.0-9 FALSE FALSE 2023-05-17 CRAN (R 4.1.3)
digest digest 0.6.31 0.6.31 FALSE FALSE 2022-12-11 CRAN (R 4.1.3)
dplyr dplyr 1.1.2 1.1.2 TRUE FALSE 2023-04-20 CRAN (R 4.1.3)
ellipsis ellipsis 0.3.2 0.3.2 FALSE FALSE 2021-04-29 CRAN (R 4.1.3)
evaluate evaluate 0.21 0.21 FALSE FALSE 2023-05-05 CRAN (R 4.1.3)
fansi fansi 1.0.4 1.0.4 FALSE FALSE 2023-01-22 CRAN (R 4.1.3)
fastmap fastmap 1.1.1 1.1.1 FALSE FALSE 2023-02-24 CRAN (R 4.1.3)
fitdistrplus fitdistrplus 1.1.11 1.1-11 FALSE FALSE 2023-04-25 CRAN (R 4.1.3)
future future 1.32.0 1.32.0 FALSE FALSE 2023-03-07 CRAN (R 4.1.3)
future.apply future.apply 1.11.0 1.11.0 FALSE FALSE 2023-05-21 CRAN (R 4.1.3)
generics generics 0.1.3 0.1.3 FALSE FALSE 2022-07-05 CRAN (R 4.1.3)
ggplot2 ggplot2 3.4.2 3.4.2 TRUE FALSE 2023-04-03 CRAN (R 4.1.3)
ggrepel ggrepel 0.9.3 0.9.3 FALSE FALSE 2023-02-03 CRAN (R 4.1.3)
ggridges ggridges 0.5.4 0.5.4 FALSE FALSE 2022-09-26 CRAN (R 4.1.3)
globals globals 0.16.2 0.16.2 FALSE FALSE 2022-11-21 CRAN (R 4.1.3)
glue glue 1.6.2 1.6.2 FALSE FALSE 2022-02-24 CRAN (R 4.1.3)
goftest goftest 1.2.3 1.2-3 FALSE FALSE 2021-10-07 CRAN (R 4.1.3)
gridExtra gridExtra 2.3 2.3 FALSE FALSE 2017-09-09 CRAN (R 4.1.3)
gtable gtable 0.3.3 0.3.3 FALSE FALSE 2023-03-21 CRAN (R 4.1.3)
scales scales 1.2.1 1.2.1 FALSE FALSE 2022-08-20 CRAN (R 4.1.3)
scattermore scattermore 1.1 1.1 FALSE FALSE 2023-05-17 CRAN (R 4.1.3)
sctransform sctransform 0.3.5 0.3.5 TRUE FALSE 2022-09-21 CRAN (R 4.1.3)
sessioninfo sessioninfo 1.2.2 1.2.2 FALSE FALSE 2021-12-06 CRAN (R 4.3.1)
Seurat Seurat 4.0.3 4.0.3 TRUE FALSE 2021-06-10 CRAN (R 4.1.0)
SeuratDisk SeuratDisk 0.0.0.9021 0.0.0.9021 TRUE FALSE 2024-08-12 Github (mojaveazure/seurat-disk@877d4e18ab38c686f5db54f8cd290274ccdbe295)
SeuratObject SeuratObject 4.1.3 4.1.3 TRUE FALSE 2022-11-07 CRAN (R 4.1.3)
shiny shiny 1.7.4 1.7.4 FALSE FALSE 2022-12-15 CRAN (R 4.1.3)
sp sp 1.6.1 1.6-1 FALSE FALSE 2023-05-31 CRAN (R 4.1.3)
spatstat.core spatstat.core 2.4.4 2.4-4 FALSE FALSE 2022-05-18 CRAN (R 4.1.3)
spatstat.data spatstat.data 3.0.1 3.0-1 FALSE FALSE 2023-03-12 CRAN (R 4.1.3)
spatstat.geom spatstat.geom 3.2.1 3.2-1 FALSE FALSE 2023-05-09 CRAN (R 4.1.3)
spatstat.random spatstat.random 3.1.5 3.1-5 FALSE FALSE 2023-05-11 CRAN (R 4.1.3)
spatstat.sparse spatstat.sparse 3.0.1 3.0-1 FALSE FALSE 2023-03-12 CRAN (R 4.1.3)
spatstat.utils spatstat.utils 3.0.3 3.0-3 FALSE FALSE 2023-05-09 CRAN (R 4.1.3)
stringi stringi 1.7.6 1.7.6 FALSE FALSE 2021-11-29 CRAN (R 4.1.1)
stringr stringr 1.5.0 1.5.0 FALSE FALSE 2022-12-02 CRAN (R 4.1.3)
survival survival 3.5.5 3.5-5 FALSE FALSE 2023-03-12 CRAN (R 4.1.3)
tensor tensor 1.5 1.5 FALSE FALSE 2012-05-05 CRAN (R 4.1.3)
tibble tibble 3.2.1 3.2.1 FALSE FALSE 2023-03-20 CRAN (R 4.1.3)
tidyr tidyr 1.3.0 1.3.0 FALSE FALSE 2023-01-24 CRAN (R 4.1.3)
tidyselect tidyselect 1.2.0 1.2.0 FALSE FALSE 2022-10-10 CRAN (R 4.1.3)
utf8 utf8 1.2.3 1.2.3 FALSE FALSE 2023-01-31 CRAN (R 4.1.3)
uuid uuid 1.1.0 1.1-0 FALSE FALSE 2022-04-19 CRAN (R 4.1.3)
uwot uwot 0.1.14 0.1.14 FALSE FALSE 2022-08-22 CRAN (R 4.1.3)
vctrs vctrs 0.6.2 0.6.2 FALSE FALSE 2023-04-19 CRAN (R 4.1.3)
viridisLite viridisLite 0.4.1 0.4.1 FALSE FALSE 2022-08-22 CRAN (R 4.1.3)
withr withr 2.5.0 2.5.0 FALSE FALSE 2022-03-03 CRAN (R 4.1.3)
xtable xtable 1.8.4 1.8-4 FALSE FALSE 2019-04-21 CRAN (R 4.1.3)
zoo zoo 1.8.12 1.8-12 FALSE FALSE 2023-04-13 CRAN (R 4.1.3)
I don't own the codes. They are copied from this github repo along with this peer reviewed paper
The original author was invited as the collaborator of this repo.