Last updated: 2021-11-15

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Knit directory: KEJP_2020_splatPop/

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    Modified:   code/plot_functions.R

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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: 103
if(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.

Version Author Date
116e4a3 cazodi 2021-10-08
bd0c8b0 cazodi 2021-05-17
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.

Version Author Date
116e4a3 cazodi 2021-10-08
bd0c8b0 cazodi 2021-05-17
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.

Version Author Date
116e4a3 cazodi 2021-10-08
bd0c8b0 cazodi 2021-05-17
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