qvalue sharing

eGene_numbers <- data.frame( 
  set = c("Microglia MFG", "Microglia STG", "Microglia THA", "Microglia SVZ", "Microglia all regions"),
  n = c(267, 769, 196, 94, 1239),
  stringsAsFactors = FALSE
)

ext_datasets <- data.frame(
  target_name = c( "Microglia Young",  "Monocytes Fairfax", "Monocytes MyND",  "DLPFC ROSMAP" ),
  alt_target_name = c("Microglia\n(Young)", "Monocytes\n(Fairfax)", "Monocytes\n(Navarro)", "Brain - DLPFC\n(ROSMAP)")
)


qvalues<- read_tsv("data/all_qvalue_merged.0.1.tsv")

## Parsed with column specification:
## cols(
##   source_name = col_character(),
##   target_name = col_character(),
##   pi1 = col_double()
## )

qvalue_matrix <- 
  qvalues %>% 
  mutate(pi1 = ifelse(is.na(pi1), yes = 1, no = pi1)) %>%
  mutate(pi1 = ifelse( source_name == target_name, yes = 1, no = pi1)) %>%
  tidyr::spread(key = target_name, value = pi1) %>% 
  column_to_rownames(var = "source_name")


qvalues_to_plot <-
  qvalues %>%
  mutate(pi1 = ifelse(is.na(pi1), yes = 1, no = pi1)) %>%
  mutate(pi1 = round(pi1, digits = 2)) %>%
  mutate(pi1 = ifelse( source_name == target_name, yes = 1, no = pi1))


# Regions with themselves
qvalues_region <- filter(qvalues_to_plot, target_name %in% c("Microglia_STG", "Microglia_MFG", "Microglia_THA", "Microglia_SVZ")) %>%
  mutate(source_name = gsub("_", " ", source_name), target_name = gsub("_", " ", target_name))

qvalues_region %>%
  ggplot(aes(x= source_name, y = target_name, fill = pi1, label = pi1)) + geom_tile() + geom_text() +
  labs(x = "discovery", y = "replication") +
  scale_fill_distiller(expression(pi[1]), type = "div", palette = "RdYlBu", limits = c(0,1) ) +
  #theme_classic() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  coord_flip() +
  scale_x_discrete(expand = c(0,0)) + scale_y_discrete( expand = c(0,0))

# Regions with external data
qvalues_external <- filter(qvalues_to_plot, !target_name %in% c("Microglia_STG", "Microglia_MFG", "Microglia_THA", "Microglia_SVZ", "Microglia_all_regions")) %>%
  mutate(source_name = gsub("_", " ", source_name), target_name = gsub("_", " ", target_name)) %>%
  left_join(eGene_numbers, by = c("source_name" = "set")) %>%
  mutate(source_name = gsub("Microglia ", "", source_name)) %>%
  mutate(source_name = ifelse(source_name == "all regions", yes = "MASHR\nshared eQTL", no = source_name)) %>%
  mutate(source_name = paste0(source_name, "\n(", n, ")" ))


#external_order <- ext_datasets$alt_name

p_ext <- 
  qvalues_external %>%
  left_join(ext_datasets, by = "target_name") %>%
  mutate(alt_target_name = factor(alt_target_name, levels = ext_datasets$alt_target_name)) %>%
  ggplot(aes(x= source_name, y = alt_target_name, fill = pi1, label = pi1)) + geom_tile() + geom_text() +
  labs(x = "Discovery", y = "Replication") +
  scale_fill_distiller(expression(pi[1]), type = "div", palette = "RdYlBu", limits = c(0,1) ) +
  #theme_classic() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  coord_flip() +
  scale_x_discrete(expand = c(0,0)) + scale_y_discrete( expand = c(0,0)) +
  geom_vline(xintercept = 1.5, size = 1) +
  theme(axis.text = element_text(colour = "black"), axis.ticks = element_line(colour = "black"))

p_ext

ggsave(plot = p_ext, filename = c("plots/qvalue_external_data.pdf"), width = 6, height = 4)