brainfo / visiumr

R source file containing for analysing 10x visium data

visiumR

R source file which contains functions

1. to run spatial clustering and markers finding for each sample. Thus easy to be applied on any samples
2. to integrate samples and annotate the cell types
3. 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 × 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)

Ackowledgement

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.