In davemcg/eyeIntegration_app: eyeIntegration Shiny App Code

Load libraries, connect to 2019 SQLite DB

library(pool)
library(tidyverse)
library(RSQLite)
library(ggrepel)

# edit this to match the path of the 2019 Eye on a Disk dataset (EOAD - "E Ode"?)
# you can get this database here:
# https://github.com/davemcg/eyeIntegration_app
pool <- dbPool(drv = SQLite(), dbname = "/Volumes/data/projects/nei/mcgaughey/auto_eyeIntegration/results/eyeIntegration_human_expression_2019_v100.sqlite")

Tables in 2019 dataset

pool %>% dbListTables() %>% as_tibble()

Load in t-SNE coordinates (and attached metadata)

For perplexity 50

tsne_50 <- pool %>% tbl('tSNE_bulk_RNA') %>% 
  filter(perplexity == 50) %>% as_tibble()
tsne_50 %>% colnames() %>% enframe()

Plot Eldred Organoid Retina against all other samples

tsne_50 %>% mutate(Organoid = case_when(grepl("Organoid", Sub_Tissue) ~ "Organoid",
                                        TRUE ~ "Not Organoid")) %>% 
  ggplot(aes(x=X1, y=X2, colour = Organoid)) +
  geom_point() + theme_minimal()

Now just Retina

tsne_50 %>% 
  mutate(Organoid = case_when(grepl("Organoid", Sub_Tissue) ~ "Organoid",
                              TRUE ~ "Not Organoid")) %>% 
  filter(Tissue == 'Retina') %>% 
  ggplot(aes(x=X1, y=X2, colour = Organoid, shape = Sub_Tissue)) +
  geom_point() + theme_minimal()

Now show the ages of the Organoids

We see the little outlier group are age 10 and 20 day organoids. Everything older looks very "retina" like (clusters closely to the fetal and stem cell based retina).

tsne_50 %>% 
  mutate(Organoid = case_when(grepl("Organoid", Sub_Tissue) ~ "Organoid",
                              TRUE ~ "Not Organoid")) %>% 
  filter(Tissue == 'Retina') %>% 
  mutate(sample_attribute = case_when(grepl("Organoid", Sub_Tissue) ~ sample_attribute,
                                      TRUE ~ "")) %>% 
  rowwise() %>% 
  mutate(Age = as.numeric(str_split(sample_attribute, '_')[[1]][2])) %>% 
  ggplot(aes(x=X1, y=X2, colour = as.factor(Age), shape = Sub_Tissue)) +
  geom_jitter() + theme_minimal()

What are the Day 10 and 20 organoid grouped with?

They are near (undifferentiated) human stem cells and some lens stem cells (which I would guess are not well differentiated?).

So it appears that in the Eldred/Johnston differentiation process, the "retina-ness" shift is happening between 20-35 days.

Another shift happens between 69 and 111 days (look at above plot).

tsne_50 %>% 
  mutate(Organoid = case_when(grepl("Organoid", Sub_Tissue) ~ "Organoid",
                              TRUE ~ "Not Organoid")) %>% 
  filter(X1 > 29 & X1 < 33) %>% 
  mutate(sample_attribute = case_when(grepl("Organoid", Sub_Tissue) ~ sample_attribute,
                                      TRUE ~ "")) %>% 
  rowwise() %>% 
  mutate(Age = as.numeric(str_split(sample_attribute, '_')[[1]][2])) %>% 
  ggplot(aes(x=X1, y=X2, colour = as.factor(Age), shape = Sub_Tissue)) +
  geom_point() + theme_minimal()