{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
This repository contains all the functions to perform Tilted-CCA (version 1.0.0.001 as of October 4, 2022) and the downstream analysis, for the paper “Quantifying common and distinct information in single-cell multimodal data with Tilted-CCA”. See the companion GitHub package https://github.com/linnykos/tiltedCCA_analysis for all the analyses performed in the paper.
This code was developed and tested primarily on R 4.1.2. on a Macbook (macOS 11.6.8 Big Sur) equipped with an i7 processor.
Tutorials and vignettes
Please see https://linnykos.github.io/tiltedCCA/ for in-depth tutorials and vignettes on how to use Tilted-CCA.
Installation
This package can be installed through devtools in R.
library("devtools")
devtools::install_github("linnykos/tiltedCCA")The package itself depends on several packages. These include dbscan, ggplot2, ggrepel, irlba, MASS, Matrix, quadprog, RANN, RColorBrewer, RSpectra, scales, Seurat, SeuratObject, and sparseMatrixStats. See the last section of this README to see where (i.e., CRAN, Bioconductor, or GitHub) to download all such packages.
After installation of all the dependencies, the installation of the tiltedCCA package itself is fast (less than 2 minutes).
Known installation issues and the solutions
(Solution posted on December 24, 2023): If you come across the error,
Error in irlba::irlba() :
function 'as_cholmod_sparse' not provided by package 'Matrix'then it is likely you need to downgrade your version of Matrix to 1.6-1.1. See https://github.com/satijalab/seurat/issues/7983. Hence, in the R console,
> remove.packages("SeuratObject")
> remotes::install_version("SeuratObject", version = "5.0.0")
> remove.packages("Matrix")
> remotes::install_version("Matrix", version = "1.6-1.1")Small simulated dataset to demo the software
See https://github.com/linnykos/tiltedCCA_analysis/tree/master/simulation for the small demo on how to use Tilted-CCA.
Setup
The following shows the suggested package versions that the developer (GitHub username: linnykos) used when developing the Tilted-CCA package.
> devtools::session_info()
─ Session info ─────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os Red Hat Enterprise Linux
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2022-10-04
pandoc 1.12.3.1 @ /usr/bin/pandoc
─ Packages ─────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.2)
brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.2)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.2)
callr 3.7.1 2022-07-13 [1] CRAN (R 4.1.2)
cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.2)
cluster 2.1.2 2021-04-17 [2] CRAN (R 4.1.2)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.2)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.2)
crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.2)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.2)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.2)
dbscan * 1.1-10 2022-01-15 [1] CRAN (R 4.1.2)
deldir 1.0-6 2021-10-23 [1] CRAN (R 4.1.2)
devtools 2.4.4 2022-07-20 [1] CRAN (R 4.1.2)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2)
dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.1.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2)
fitdistrplus 1.1-8 2022-03-10 [1] CRAN (R 4.1.2)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2)
future 1.27.0 2022-07-22 [1] CRAN (R 4.1.2)
future.apply 1.9.0 2022-04-25 [1] CRAN (R 4.1.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.2)
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.1.2)
ggrepel * 0.9.1 2021-01-15 [1] CRAN (R 4.1.2)
ggridges 0.5.3 2021-01-08 [1] CRAN (R 4.1.2)
globals 0.16.0 2022-08-05 [1] CRAN (R 4.1.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.1.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.2)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.1.2)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.2)
httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.1.2)
httr 1.4.3 2022-05-04 [1] CRAN (R 4.1.2)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.1.2)
igraph 1.3.4 2022-07-19 [1] CRAN (R 4.1.2)
irlba * 2.3.5 2021-12-06 [1] CRAN (R 4.1.2)
jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.1.2)
KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.1.2)
later 1.3.0 2021-08-18 [1] CRAN (R 4.1.2)
lattice 0.20-45 2021-09-22 [2] CRAN (R 4.1.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.2)
leiden 0.4.2 2022-05-09 [1] CRAN (R 4.1.2)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2)
listenv 0.8.0 2019-12-05 [1] CRAN (R 4.1.2)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.1.2)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.2)
MASS * 7.3-54 2021-05-03 [2] CRAN (R 4.1.2)
Matrix * 1.3-4 2021-06-01 [2] CRAN (R 4.1.2)
MatrixGenerics * 1.6.0 2021-10-26 [1] Bioconductor
matrixStats * 0.62.0 2022-04-19 [1] CRAN (R 4.1.2)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.2)
mgcv 1.8-38 2021-10-06 [2] CRAN (R 4.1.2)
mime 0.12 2021-09-28 [1] CRAN (R 4.1.2)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.1.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2)
nlme 3.1-153 2021-09-07 [2] CRAN (R 4.1.2)
parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.1.2)
patchwork 1.1.1 2020-12-17 [1] CRAN (R 4.1.2)
pbapply 1.5-0 2021-09-16 [1] CRAN (R 4.1.2)
pillar 1.8.0 2022-07-18 [1] CRAN (R 4.1.2)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2)
pkgload 1.3.0 2022-06-27 [1] CRAN (R 4.1.2)
plotly 4.10.0 2021-10-09 [1] CRAN (R 4.1.2)
plyr 1.8.7 2022-03-24 [1] CRAN (R 4.1.2)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.2)
polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.1.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.2)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.1.2)
profvis 0.3.7 2020-11-02 [1] CRAN (R 4.1.2)
progressr 0.10.1 2022-06-03 [1] CRAN (R 4.1.2)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.2)
ps 1.7.0 2022-04-23 [1] CRAN (R 4.1.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.2)
quadprog * 1.5-8 2019-11-20 [1] CRAN (R 4.1.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2)
RANN * 2.6.1 2019-01-08 [1] CRAN (R 4.1.2)
RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.1.2)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.1.2)
RcppAnnoy 0.0.19 2021-07-30 [1] CRAN (R 4.1.2)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.2)
reticulate 1.25 2022-05-11 [1] CRAN (R 4.1.2)
rgeos 0.5-9 2021-12-15 [1] CRAN (R 4.1.2)
rlang 1.0.4 2022-07-12 [1] CRAN (R 4.1.2)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.1.2)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.2)
RSpectra * 0.16-1 2022-04-24 [1] CRAN (R 4.1.2)
Rtsne 0.16 2022-04-17 [1] CRAN (R 4.1.2)
scales * 1.2.0 2022-04-13 [1] CRAN (R 4.1.2)
scattermore 0.8 2022-02-14 [1] CRAN (R 4.1.2)
sctransform 0.3.3 2022-01-13 [1] CRAN (R 4.1.2)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2)
Seurat * 4.1.1 2022-05-02 [1] CRAN (R 4.1.2)
SeuratObject * 4.1.0 2022-05-01 [1] CRAN (R 4.1.2)
shiny 1.7.2 2022-07-19 [1] CRAN (R 4.1.2)
sp * 1.5-0 2022-06-05 [1] CRAN (R 4.1.2)
sparseMatrixStats * 1.6.0 2021-10-26 [1] Bioconductor
spatstat.core 2.4-2 2022-04-01 [1] CRAN (R 4.1.2)
spatstat.data 2.2-0 2022-04-18 [1] CRAN (R 4.1.2)
spatstat.geom 2.4-0 2022-03-29 [1] CRAN (R 4.1.2)
spatstat.random 2.2-0 2022-03-30 [1] CRAN (R 4.1.2)
spatstat.sparse 2.1-1 2022-04-18 [1] CRAN (R 4.1.2)
spatstat.utils 2.3-1 2022-05-06 [1] CRAN (R 4.1.2)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.2)
survival 3.2-13 2021-08-24 [2] CRAN (R 4.1.2)
tensor 1.5 2012-05-05 [1] CRAN (R 4.1.2)
testthat * 3.1.4 2022-04-26 [1] CRAN (R 4.1.2)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.2)
tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2)
tiltedCCA * 1.0.0.001 2022-09-06 [1] local
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.1.2)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.1.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2)
uwot 0.1.13 2022-08-16 [1] CRAN (R 4.1.2)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.2)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.2)
zoo 1.8-10 2022-04-15 [1] CRAN (R 4.1.2)