Compares gene annotations between two different cell time types

Goal

1. Compare cell time estimates derived from algebraic methods versus from trignometric transformation.

2. Do same for cell times based on FUCCI and cell times based on FUCCI and DAPI.

Getting data

library(Biobase)
df <- readRDS(file="../data/eset-final.rds")
pdata <- pData(df)
fdata <- fData(df)

# select endogeneous genes
counts <- exprs(df)[grep("ENSG", rownames(df)), ]

log2cpm.all <- t(log2(1+(10^6)*(t(counts)/pdata$molecules)))

#macosko <- readRDS("data/cellcycle-genes-previous-studies/rds/macosko-2015.rds")
counts <- counts[,order(pdata$theta)]
log2cpm.all <- log2cpm.all[,order(pdata$theta)]
pdata <- pdata[order(pdata$theta),]

log2cpm.quant <- readRDS("../output/npreg-trendfilter-quantile.Rmd/log2cpm.quant.rds")


pca_double <- prcomp(cbind(pdata$gfp.median.log10sum.adjust,
                           pdata$rfp.median.log10sum.adjust), scale. = T)
pca_triple <- prcomp(cbind(pdata$gfp.median.log10sum.adjust,
                           pdata$rfp.median.log10sum.adjust,
                           pdata$dapi.median.log10sum.adjust), scale. = T)

library(circular)
theta_triple <- as.numeric(coord2rad(pca_triple$x[,1:2]))
theta_double <- as.numeric(coord2rad(pca_double$x[,1:2]))
names(theta_triple) <- rownames(pdata)
names(theta_double) <- rownames(pdata)

Cell times based on FUCCI only

source("../peco/R/intensity2circle.R")
library(conicfit)
par(mfrow=c(1,1))
df <- cbind(pdata$gfp.median.log10sum.adjust,
            pdata$rfp.median.log10sum.adjust)
ang <- intensity2circle(df, plot.it = TRUE)

par(mfrow=c(1,1))
source("../peco/R/cycle.corr.R")
ang_shift <- rotation(theta_double, ang)
par(mfrow=c(2,2))
plot(x=theta_double[order(theta_double)],
     y=pdata$gfp.median.log10sum.adjust[order(theta_double)], col="forestgreen",
     ylab="log intensity", xlab="Cell time estimates",
     main = "trignometry", ylim=c(-1, 1))
points(x=theta_double[order(theta_double)],
       y=pdata$rfp.median.log10sum.adjust[order(theta_double)], col="red")
points(x=theta_double[order(theta_double)],
       y=pdata$dapi.median.log10sum.adjust[order(theta_double)], col="blue")

plot(x=ang_shift[order(ang_shift)],
     y=pdata$gfp.median.log10sum.adjust[order(ang_shift)], col="forestgreen",
     main = "algebra", ylim=c(-1, 1))     
points(x=ang_shift[order(ang_shift)],
     y=pdata$rfp.median.log10sum.adjust[order(ang_shift)], col="red")
points(x=ang_shift[order(ang_shift)],
       y=pdata$dapi.median.log10sum.adjust[order(ang_shift)], col="blue")

plot(ang_shift, theta_double,
     xlab="trigometry-based",
     ylab="algebra-based", main="Compar angles"); abline(0,1, col="blue")

Cell times based on FUCCI and DAPI only

# algebraic methods
source("../peco/R/intensity2circle.R")
library(conicfit)
par(mfrow=c(1,1))
df <- cbind(pdata$gfp.median.log10sum.adjust,
                           pdata$rfp.median.log10sum.adjust,
                           pdata$dapi.median.log10sum.adjust)
ang <- intensity2circle(df, plot.it = TRUE)

par(mfrow=c(2,2))
source("../peco/R/cycle.corr.R")
ang_shift <- rotation(theta_triple, ang)
ang_shift <- ang_shift%%(2*pi)
plot(x=theta_triple[order(theta_triple)],
     y=pdata$gfp.median.log10sum.adjust[order(theta_triple)], col="forestgreen",
     ylab="log intensity", xlab="Cell time estimates",
     main = "trignometry", ylim=c(-1, 1))
points(x=theta_triple[order(theta_triple)],
       y=pdata$rfp.median.log10sum.adjust[order(theta_triple)], col="red")
points(x=theta_triple[order(theta_triple)],
       y=pdata$dapi.median.log10sum.adjust[order(theta_triple)], col="blue")

plot(x=ang_shift[order(ang_shift)],
     y=pdata$gfp.median.log10sum.adjust[order(ang_shift)], col="forestgreen",
     main = "algebra", ylim=c(-1, 1))     
points(x=ang_shift[order(ang_shift)],
     y=pdata$rfp.median.log10sum.adjust[order(ang_shift)], col="red")
points(x=ang_shift[order(ang_shift)],
       y=pdata$dapi.median.log10sum.adjust[order(ang_shift)], col="blue")

plot(ang_shift, theta_triple,
     xlab="trigometry-based",
     ylab="algebra-based", main="Compar angles"); abline(0,1, col="blue")

Session information

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] conicfit_1.0.4      geigen_2.2          pracma_2.1.1       
[4] circular_0.4-93     Biobase_2.38.0      BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17    mvtnorm_1.0-8   digest_0.6.15   rprojroot_1.3-2
 [5] backports_1.1.2 git2r_0.21.0    magrittr_1.5    evaluate_0.10.1
 [9] stringi_1.1.6   boot_1.3-20     rmarkdown_1.10  tools_3.4.3    
[13] stringr_1.2.0   yaml_2.1.16     compiler_3.4.3  htmltools_0.3.6
[17] knitr_1.20