Data driven prior from ED
Yuxin Zou
12/21/2020
Last updated: 2021-03-07
Checks: 7 0
Knit directory: mmbr-rss-dsc/
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The result is from this notebook.
Artificial mixture
dat_a = readRDS('data/mmbr_ukb_simulation/artificial_mixture_ukb.FL_PC3.EDudr.rds')
names(dat_a)[1] "U" "w" "loglik"names(dat_a$w) = names(dat_a$U)
barplot(dat_a$w, las=2, cex.names = 0.7)
tol = 1E-15
names(dat_a$U)[which(dat_a$w>tol)][1] "FLASH_3" "FLASH_4" "tFLASH" "tPCA" "XX" The component with strongest weight is tXX.
plot_sharing = function(X) {
clrs <- colorRampPalette(rev(c("#D73027","#FC8D59","#FEE090","#FFFFBF",
"#E0F3F8","#91BFDB","#4575B4")))(128)
# lat <- cov2cor(X)
lat <- X/max(diag(X))
lat[lower.tri(lat)] <- NA
n <- nrow(lat)
print(lattice::levelplot(lat[n:1,],col.regions = clrs,xlab = "",ylab = "",
colorkey = TRUE,at = seq(-1,1,length.out = 128),
scales = list(cex = 0.6,x = list(rot = 45))))
}plot_sharing(dat_a$U$XX)
plot_sharing(dat_a$U$tFLASH)
plot_sharing(dat_a$U$FLASH_3)
plot_sharing(dat_a$U$FLASH_4)
UKB bloodcells mixture
dat_ukb = readRDS('data/mmbr_ukb_simulation/ukb_bloodcells_mixture.FL_PC3.EDudr.rds')names(dat_ukb$w) = names(dat_ukb$U)
barplot(dat_ukb$w, las=2, cex.names = 0.7)
names(dat_ukb$U)[which(dat_ukb$w>tol)] [1] "FLASH_1" "FLASH_3" "FLASH_4" "FLASH_5" "FLASH_6" "FLASH_8" "FLASH_9"
[8] "tFLASH" "PCA_2" "tPCA" "XX" plot_sharing(dat_ukb$U$XX)
plot_sharing(dat_ukb$U$FLASH_8)
plot_sharing(dat_ukb$U$tFLASH)
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 whisker_0.4 knitr_1.30 magrittr_2.0.1
[5] lattice_0.20-41 R6_2.5.0 rlang_0.4.10 stringr_1.4.0
[9] tools_4.0.3 grid_4.0.3 xfun_0.19 git2r_0.27.1
[13] htmltools_0.5.0 ellipsis_0.3.1 yaml_2.2.1 digest_0.6.27
[17] rprojroot_2.0.2 tibble_3.0.6 lifecycle_1.0.0 crayon_1.4.1
[21] later_1.1.0.1 vctrs_0.3.6 promises_1.1.1 fs_1.5.0
[25] glue_1.4.2 evaluate_0.14 rmarkdown_2.5 stringi_1.5.3
[29] compiler_4.0.3 pillar_1.4.7 httpuv_1.5.4 pkgconfig_2.0.3