10x NeuroSeq: Simulations
Christina B. Azodi
2021-11-15
Last updated: 2021-11-15
Checks: 6 1
Knit directory: KEJP_2020_splatPop/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 116e4a3 | cazodi | 2021-10-08 | update mean-variance plots for manuscript |
| html | 116e4a3 | cazodi | 2021-10-08 | update mean-variance plots for manuscript |
| Rmd | bd0c8b0 | cazodi | 2021-05-17 | updates to 10x neuroseq and ss2 ipsc examples |
| html | bd0c8b0 | cazodi | 2021-05-17 | updates to 10x neuroseq and ss2 ipsc examples |
#install.packages("/mnt/mcscratch/cazodi/Software/splatter_1.15.2.tar.gz", repos = NULL, type="source")
suppressPackageStartupMessages({
library(SingleCellExperiment)
library(scater)
library(tidyverse)
#detach("package:splatter", unload=TRUE)
library(splatter)
library(VariantAnnotation)
library(cluster)
library(fitdistrplus)
library(RColorBrewer)
library(ggpubr)
library(cowplot)
})
source("code/plot_functions.R")
source("code/misc_functions.R")date <- Sys.Date()
set.seed(42)
n.genes <- 504
save <- TRUE
rerun <- FALSE
date.use <- "2021-05-17"
nSamples <- 6
sample.colors <- projectColors("samples")
# Chromosome 22 data
gff <- read.table("references/chr22.genes.gff3", sep="\t", header=FALSE, quote="")
vcf <- readVcf("references/chr22.filtered.vcf", "hg38")
sampleNames <- colnames(geno(vcf)$GT)
# Smartseq2 iPSC data and splatPopParams
sce <- readRDS("data/sce_Neuro-10x_2CT.rds")
sce$Batch <- "Batch1"
params <- readRDS("output/01_sims/splatPop-params_Neuro-10x.rds")Simple simulation
sce.simple <- subset(sce, , Group == "FPP" &
Sample %in% sample(unique(sce$Sample), nSamples))
nCells <- as.data.frame(colData(sce.simple)) %>%
group_by(Sample) %>% dplyr::count()
nCells <- round(mean(nCells$n))
message("average nCells in empirical data: ", nCells)average nCells in empirical data: 103if(rerun) {
vcf.simple <- vcf[, sample(sampleNames, nSamples)]
params.simple <- setParams(params,
similarity.scale = 2,
batchCells = c(nCells))
sim.simple <- splatPopSimulate(vcf = vcf.simple,
gff = gff,
params = params.simple,
sparsify = FALSE)
} else{
sim.simple <- readRDS(paste0("output/01_sims/", date.use, "_simple-10x.rds"))
}
plotComparisons(sim=sim.simple, emp=sce.simple, maxCells=50,
mv.nCells = c(5, 20, 50), mv.y.max = 0.35) `geom_smooth()` using formula 'y ~ x'`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
if(save){
save.name <- paste0(date, "_simple-10x")
saveRDS(sim.simple, paste0("output/01_sims/", save.name, ".rds"))
ggsave(paste0("output/00_Figures/", save.name, ".pdf"), width = 6, height = 7)
}Group effects
Simple example
vcf.group.simple <- vcf[, sample(sampleNames, nSamples)]
if(rerun) {
params.group.simple <- setParams(params, batchCells=40,
eqtl.n = 0.5,
group.prob = c(0.5, 0.5),
eqtl.group.specific = 0.5,
de.prob = 0.5,
de.facLoc = 0.5,
de.facScale = 0.75)
sim.group.simple <- splatPopSimulate(vcf = vcf.group.simple, gff = gff,
params = params.group.simple,
sparsify = FALSE)
} else{
sim.group.simple <- readRDS(paste0("output/01_sims/", date.use, "_example-groups.rds"))
}
plotSims(sim=sim.group.simple, variables = c("Sample", "Group"),
colour_by = "Sample", shape_by= "Group")Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
if(save){
save.name <- paste0(date, "_example-groups")
saveRDS(sim.group.simple, paste0("output/01_sims/", save.name, ".rds"))
ggsave(paste0("output/00_Figures/", save.name, ".pdf"), width = 3, height = 5)
}10x - Cell-groups
sce.groups <- subset(sce, , Sample %in% sample(unique(sce$Sample), nSamples))
if(rerun){
group.prob <- unname(table(sce.groups$Group) / ncol(sce.groups))
group.prob <- c(0.773578, 0.226422)
nCells.SB <- as.list(data.frame(table(sce$Sample)))$Freq
nC.fit <- fitdist(nCells.SB, "gamma")
vcf.groups <- vcf[, sample(sampleNames, nSamples)]
params.groups <- setParams(params,
# population description parameters
nCells.sample = TRUE,
nCells.shape = nC.fit$estimate["shape"],
nCells.rate = nC.fit$estimate["rate"],
# parameters specifying effects
eqtl.n = 1,
similarity.scale = 2,
group.prob = group.prob,
eqtl.group.specific = 0.5,
de.prob = 0.5,
de.facLoc = 0.6,
de.facScale = 0.5)
sim.groups <- splatPopSimulate(vcf = vcf.groups, gff = gff,
params = params.groups, sparsify = FALSE)
} else{
sim.groups <- readRDS(paste0("output/01_sims/", date.use, "_10x-groups.rds"))
}
plotComparisons(sim=sim.groups, emp=sce.groups,
maxCells = 30,
variables = c("Sample", "Group"),
colour_by = "Sample",
shape_by= "Group",
samp.col = sample.colors,
mv.nCells = c(5, 20, NA),
mv.y.max = 0.7)`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
if(save){
save.name <- paste0(date, "_10x-groups")
saveRDS(sim.groups, paste0("output/01_sims/", save.name, ".rds"))
ggsave(paste0("output/00_Figures/", save.name, ".pdf"), width = 6, height = 7)
}tSNE plots
pSim <- plotTSNEx(sim.simple, colour_by="Sample",
maxCells = 50, samp.col = sample.colors)Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.pEmp<- plotTSNEx(sce.simple, colour_by="Sample",
maxCells = 50, samp.col = sample.colors) Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.pSimGroup <- plotTSNEx(sim.groups, colour_by="Sample", shape_by="Group",
maxCells = 50, samp.col = sample.colors)Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.pEmpGroup <- plotTSNEx(sce.groups, colour_by="Sample", shape_by="Group",
maxCells = 50, samp.col = sample.colors) Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.plot_grid(pEmp, pSim, pEmpGroup, pSimGroup, ncol=2, labels = "auto")
if(save){
save.name <- paste0(date, "_10x-groups-TSNEs")
ggsave(paste0("output/00_Figures/", save.name, ".pdf"), width = 6)
}Saving 6 x 10 in image
devtools::session_info()─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.1.1 (2021-08-10)
os Red Hat Enterprise Linux 8.4 (Ootpa)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Melbourne
date 2021-11-15
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.1)
AnnotationDbi 1.56.1 2021-10-29 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.1)
backports 1.3.0 2021-10-27 [1] CRAN (R 4.1.1)
beachmat 2.10.0 2021-10-26 [1] Bioconductor
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.1.1)
Biobase * 2.54.0 2021-10-26 [1] Bioconductor
BiocFileCache 2.2.0 2021-10-26 [1] Bioconductor
BiocGenerics * 0.40.0 2021-10-26 [1] Bioconductor
BiocIO 1.4.0 2021-10-26 [1] Bioconductor
BiocNeighbors 1.12.0 2021-10-26 [1] Bioconductor
BiocParallel 1.28.0 2021-10-26 [1] Bioconductor
BiocSingular 1.10.0 2021-10-26 [1] Bioconductor
biomaRt 2.50.0 2021-10-26 [1] Bioconductor
Biostrings * 2.62.0 2021-10-26 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.1)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.1)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.1)
blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.1)
broom 0.7.10 2021-10-31 [1] CRAN (R 4.1.1)
BSgenome 1.62.0 2021-10-26 [1] Bioconductor
bslib 0.3.1 2021-10-06 [1] CRAN (R 4.1.1)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.0.4)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1)
car 3.0-11 2021-06-27 [1] CRAN (R 4.1.1)
carData 3.0-4 2020-05-22 [1] CRAN (R 4.1.1)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.1)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.1)
cli 3.0.1 2021-07-17 [1] CRAN (R 4.0.4)
cluster * 2.1.2 2021-04-17 [2] CRAN (R 4.1.1)
colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.1)
cowplot * 1.1.1 2020-12-30 [1] CRAN (R 4.1.1)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1)
curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.1)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.0.4)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.1)
dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.1.1)
DelayedArray 0.20.0 2021-10-26 [1] Bioconductor
DelayedMatrixStats 1.12.3 2021-02-03 [1] Bioconductor
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.1)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.1)
digest 0.6.28 2021-09-23 [1] CRAN (R 4.0.4)
dplyr * 1.0.7 2021-06-18 [1] CRAN (R 4.1.1)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.1)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.1)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.1)
farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.1)
filelock 1.0.2 2018-10-05 [1] CRAN (R 4.1.1)
fitdistrplus * 1.1-6 2021-09-28 [1] CRAN (R 4.1.1)
forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.1.1)
foreign 0.8-81 2020-12-22 [2] CRAN (R 4.1.1)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.1)
generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.1)
GenomeInfoDb * 1.30.0 2021-10-26 [1] Bioconductor
GenomeInfoDbData 1.2.7 2021-11-03 [1] Bioconductor
GenomicAlignments 1.30.0 2021-10-26 [1] Bioconductor
GenomicFeatures 1.46.1 2021-10-27 [1] Bioconductor
GenomicRanges * 1.46.0 2021-10-26 [1] Bioconductor
ggbeeswarm 0.6.0 2017-08-07 [1] CRAN (R 4.1.1)
ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.1)
ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.1.1)
ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.1)
ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.1)
git2r 0.28.0 2021-01-10 [1] CRAN (R 4.1.1)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.1)
haven 2.4.3 2021-08-04 [1] CRAN (R 4.1.1)
highr 0.9 2021-04-16 [1] CRAN (R 4.1.1)
hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.1)
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.0.4)
httpuv 1.6.3 2021-09-09 [1] CRAN (R 4.1.1)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.1)
IRanges * 2.28.0 2021-10-26 [1] Bioconductor
irlba 2.3.3 2019-02-05 [1] CRAN (R 4.1.1)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.1.1)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.1)
KEGGREST 1.34.0 2021-10-26 [1] Bioconductor
knitr 1.36 2021-09-29 [1] CRAN (R 4.1.1)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.1)
later 1.3.0 2021-08-18 [1] CRAN (R 4.1.1)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.1)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1)
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.1)
lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.0.4)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.1)
MASS * 7.3-54 2021-05-03 [1] CRAN (R 4.1.1)
Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.1.1)
MatrixGenerics * 1.2.1 2021-01-30 [1] Bioconductor
matrixStats * 0.60.0 2021-07-26 [1] CRAN (R 4.0.4)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.1)
mgcv 1.8-38 2021-10-06 [1] CRAN (R 4.1.1)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.1.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.1)
nlme 3.1-153 2021-09-07 [1] CRAN (R 4.1.1)
openxlsx 4.2.4 2021-06-16 [1] CRAN (R 4.1.1)
pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.1)
pkgload 1.2.3 2021-10-13 [1] CRAN (R 4.1.1)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.1)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.1)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.1)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.1)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.1)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.1)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.1.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.1)
RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 4.1.1)
Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.1)
RCurl 1.98-1.4 2021-08-17 [1] CRAN (R 4.0.4)
readr * 2.0.2 2021-09-27 [1] CRAN (R 4.1.1)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.1.1)
remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.1)
reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.1)
restfulr 0.0.13 2017-08-06 [1] CRAN (R 4.1.1)
rio 0.5.27 2021-06-21 [1] CRAN (R 4.1.1)
rjson 0.2.20 2018-06-08 [1] CRAN (R 4.1.1)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.0.4)
rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.1)
Rsamtools * 2.10.0 2021-10-26 [1] Bioconductor
RSQLite 2.2.8 2021-08-21 [1] CRAN (R 4.0.4)
rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.1.1)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.1.1)
rtracklayer 1.54.0 2021-10-26 [1] Bioconductor
Rtsne 0.15 2018-11-10 [1] CRAN (R 4.1.1)
rvest 1.0.2 2021-10-16 [1] CRAN (R 4.1.1)
S4Vectors * 0.32.0 2021-10-26 [1] Bioconductor
sass 0.4.0 2021-05-12 [1] CRAN (R 4.1.1)
ScaledMatrix 1.2.0 2021-10-26 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.1)
scater * 1.22.0 2021-10-26 [1] Bioconductor
scuttle * 1.4.0 2021-10-26 [1] Bioconductor
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
SingleCellExperiment * 1.16.0 2021-10-26 [1] Bioconductor
sparseMatrixStats 1.2.1 2021-02-02 [1] Bioconductor
splatter * 1.18.1 2021-11-02 [1] Bioconductor
stringi 1.7.5 2021-10-04 [1] CRAN (R 4.0.4)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
SummarizedExperiment * 1.24.0 2021-10-26 [1] Bioconductor
survival * 3.2-13 2021-08-24 [1] CRAN (R 4.0.4)
testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.1)
tibble * 3.1.4 2021-08-25 [1] CRAN (R 4.0.4)
tidyr * 1.1.4 2021-09-27 [1] CRAN (R 4.0.4)
tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.1)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.1.1)
tzdb 0.2.0 2021-10-27 [1] CRAN (R 4.1.1)
usethis 2.1.3 2021-10-27 [1] CRAN (R 4.1.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.0.4)
VariantAnnotation * 1.40.0 2021-10-26 [1] Bioconductor
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.1)
vipor 0.4.5 2017-03-22 [1] CRAN (R 4.1.1)
viridis 0.6.2 2021-10-13 [1] CRAN (R 4.0.4)
viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.1)
whisker 0.4 2019-08-28 [1] CRAN (R 4.1.1)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.1)
workflowr 1.6.2 2020-04-30 [1] CRAN (R 4.1.1)
xfun 0.26 2021-09-14 [1] CRAN (R 4.0.4)
XML 3.99-0.7 2021-08-17 [1] CRAN (R 4.0.4)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2)
XVector * 0.34.0 2021-10-26 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.1)
zip 2.2.0 2021-05-31 [1] CRAN (R 4.1.1)
zlibbioc 1.40.0 2021-10-26 [1] Bioconductor
[1] /mnt/mcfiles/cazodi/R/x86_64-pc-linux-gnu-library/4.1
[2] /opt/R/4.1.1/lib/R/library