diff --git a/analysis/assess_fits_68k_pbmc.Rmd b/analysis/assess_fits_68k_pbmc.Rmd index 0d6ad10..9363cbe 100644 --- a/analysis/assess_fits_68k_pbmc.Rmd +++ b/analysis/assess_fits_68k_pbmc.Rmd @@ -23,6 +23,7 @@ library(ggplot2) library(cowplot) library(ggrepel) set.seed(1) +source("../code/plot_functions.R") ``` Load the 68k PBMC data, and the results of running `fit_poisson_nmf` @@ -232,3 +233,25 @@ ggsave("../plots/loadings_scatterplot_pbmc68k_k12.png", ggsave("../plots/structure_plot_pbmc68k.eps",p3,height = 2,width = 8) ggsave("../plots/genes_scatterplot_pbmc68k.eps",p4,height = 4,width = 4.25) ``` + +```{r elbo-plots, fig.height=6, fig.width=9} +load("../output/pbmc68k/lda-pbmc68k.RData") +p <- vector("list",12) +for (i in 2:12) { + runs <- which(dat$k == i) + p[[i]] <- create_elbo_plot(fits[runs],dat[runs,"runtime"],i) +} +plot_grid(p[[2]],p[[3]],p[[4]],p[[5]], + p[[6]],p[[7]],p[[8]],p[[9]], + p[[10]],p[[11]],p[[12]], + nrow = 3,ncol = 4) +``` + +```{r plots-for-paper-4, message=FALSE, echo=FALSE} +ggsave("../plots/lda_elbo_pbmc68k.eps", + plot_grid(p[[2]],p[[3]],p[[4]],p[[5]], + p[[6]],p[[7]],p[[8]],p[[9]], + p[[10]],p[[11]],p[[12]], + nrow = 3,ncol = 4), + height = 6,width = 9) +```