In githubz0r/SecretUtils: Some utils for Conos

library(conos)
library(tidyverse)
devtools::load_all('/home/larsc/SecretUtils')
library(cowplot)
library(splatter)
devtools::load_all('/home/viktor_petukhov/Copenhagen/NeuronalMaturation')
devtools::load_all('/home/viktor_petukhov/SmallProjects/scConditionDifference')
params <- readRDS('/home/larsc/data/splatter_lamp5_params.rds')

Maybe there's something wrong with the simulategroups function

t_res <- splatSimulateGroups(params, group.prob = rep(1/6, 6),
                                    de.prob = c(0,0,0.2,0.3,0.4, 0.5), nGenes=10000, batchCells=200*6,
                                    lib.loc=8, verbose = FALSE)
t_cm <- counts(t_res)
t_annot <- t_res@colData %>% as.data.frame
t_p2 <- GetPagoda(t_cm, n.odgenes = 3000, verbose=F, embeding.type = NULL)

t_subcms <- t_annot$Cell %>% split(t_annot$Group) %>% lapply(function(x){
  t_p2$counts[x, ]
})

t_subcms_raw <- t_annot$Cell %>% split(t_annot$Group) %>% lapply(function(x){
  t_p2$misc$rawCounts[x, ]
})

lfcs_test <- t_subcms %>% lapply(function(x){
  lfcs <- log2(Matrix::colMeans(x)/Matrix::colMeans(t_subcms$Group1))
  return(abs(lfcs[is.finite(lfcs)]))
})

lfcs_test %>% lapply(median)