Exploratory analysis of Cnr1 in mouse Onecut3-GABAergic and dopaminergic hypothalamic neurons during development

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Last updated: 2023-05-29

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Knit directory: PeVN-dopaminergic-Cnr1/

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    Modified:   analysis/eda.Rmd
    Modified:   data/oc3_fin.h5seurat
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Gpr55-Cnr1_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Gpr55-Onecut3_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Cnr1_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Ddc_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Gad1_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Gad2_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Gpr55_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Onecut2_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Prlr_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Slc32a1_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Slc6a3_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Onecut3-Th_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Slc32a1-Cnr1_.pdf
    Modified:   output/figures/stat-corr-plt_oc3-rna-data-Slc32a1-Gpr55_.pdf
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File	Version	Author	Date	Message
Rmd	aaece06	Evgenii O. Tretiakov	2023-05-29	from Romanov et al 2020 subset GABAergic and dopaminergic Onecut3 population and use Arc-TIDA for comparison
html	aaece06	Evgenii O. Tretiakov	2023-05-29	from Romanov et al 2020 subset GABAergic and dopaminergic Onecut3 population and use Arc-TIDA for comparison

---

# Load tidyverse infrastructure packages
library(here)
library(tidyverse)
library(magrittr)
library(zeallot)
library(future)

# Load packages for scRNA-seq analysis and visualisation
library(sctransform)
library(Seurat)
library(SeuratWrappers)
library(SeuratDisk)
library(scCustomize)
library(UpSetR)
library(patchwork)
library(RColorBrewer)
library(Nebulosa)

src_dir <- here("code")
data_dir <- here("data")
output_dir <- here("output")
plots_dir <- here(output_dir, "figures")
tables_dir <- here(output_dir, "tables")

source(here(src_dir, "functions.R"))
source(here(src_dir, "genes.R"))

reseed <- 42
set.seed(seed = reseed)

# available cores
n_cores <- available_cores(prop2use = .5)
# Parameters for parallel execution
plan("multicore", workers = n_cores)
options(
  future.globals.maxSize = Inf,
  future.rng.onMisuse = "ignore"
)
plan()

multicore:
- args: function (..., workers = 16, envir = parent.frame())
- tweaked: TRUE
- call: plan("multicore", workers = n_cores)

Read data

rar2020_ages_all <- c("E15", "E17", "P00", "P02", "P10", "P23")
rar2020_ages_postnat <- c("P02", "P10", "P23")
samples_df <- read_tsv(here("data/samples.tsv"))
colours_wtree <- setNames(
  read_lines(here(data_dir, "colours_wtree.tsv")),
  1:45
)

rar2020_srt_pub <-
  readr::read_rds(file.path(data_dir, "oldCCA_nae_srt.rds"))
rar2020_srt_pub %<>% UpdateSeuratObject()
colnames(rar2020_srt_pub@reductions$umap@cell.embeddings) <-
  c("UMAP_1", "UMAP_2")

rar2020_srt_pub$orig.ident <-
  rar2020_srt_pub %>%
  colnames() %>%
  str_split(pattern = ":", simplify = TRUE) %>%
  .[, 1] %>%
  plyr::mapvalues(
    x = .,
    from = samples_df$fullname,
    to = samples_df$sample
  )
rar2020_srt_pub$age <-
  plyr::mapvalues(
    x = rar2020_srt_pub$orig.ident,
    from = samples_df$sample,
    to = samples_df$age
  )
Idents(rar2020_srt_pub) <- "wtree"
neurons <-
  subset(rar2020_srt_pub, idents = c("18", "32"))
neurons <- RenameIdents(neurons, "18" = "PeVN_Onecut3", "32" = "Arc_TIDA")
neurons$celltype <- Idents(neurons)
neurons <-
  subset(neurons, subset = Slc17a6 == 0)
onecut3 <-
  subset(neurons,
    subset = Onecut3 > 0 | Th > 0 | Ddc > 0 | Slc6a3 > 0
  )

onecut3 <-
  Store_Palette_Seurat(
    seurat_object = onecut3,
    palette = rev(brewer.pal(n = 11, name = "Spectral")),
    palette_name = "div_Colour_Pal"
  )

Thus we subset the dataset to the neurons of interest from cluster 18, which are GABAergic and dopaminergic neurons expressing Onecut3 transcription factor. We also explicitly exclude Slc17a6-expressing neurons, which are glutamatergic neurons just in case to reduce noise. As the control group we use dopaminergic TIDA-neurons from the arcuate nucleus.

Derive and filter matrix of neurons of interest

mtx_oc3 <-
  onecut3 %>%
  GetAssayData("data", "RNA") %>%
  as.data.frame() %>%
  t()
rownames(mtx_oc3) <- colnames(onecut3)

# Filter features
filt_low_genes <-
  colSums(mtx_oc3) %>%
  .[. > quantile(., 0.4)] %>%
  names()
mtx_oc3 %<>% .[, filt_low_genes]

min_filt_vector <-
  mtx_oc3 %>%
  as_tibble() %>%
  select(all_of(filt_low_genes)) %>%
  summarise(across(.fns = ~ quantile(.x, .1))) %>%
  as.list() %>%
  map(as.double) %>%
  simplify() %>%
  .[colnames(mtx_oc3)]

# Prepare table of intersection sets analysis
content_mtx_oc3 <-
  (mtx_oc3 > min_filt_vector) %>%
  as_tibble() %>%
  mutate_all(as.numeric)

Plot UMAPs density

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Onecut3"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-onecut3-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Th"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Th-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Slc6a3"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Slc6a3-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Prlr"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Prlr-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Cnr1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Cnr1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Gpr55"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Gpr55-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Mgll"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Mgll-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Dagla"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Dagla-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Daglb"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Daglb-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Faah"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Faah-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Napepld"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Napepld-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Gde1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Gde1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Pparg"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Pparg-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Slc32a1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-slc32a1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Gad1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-gad1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Custom(
  seurat_object = onecut3,
  features = c("Gad2"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-gad2-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Joint density UMAP’s plots

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Onecut3", "Cnr1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Onecut3-Cnr1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Onecut3", "Th"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Onecut3-Th-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Cnr1", "Th"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Cnr1-Th-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Prlr", "Cnr1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Prlr-Cnr1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Prlr", "Th"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Prlr-Th-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Prlr", "Onecut3"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Prlr-Onecut3-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Gpr55", "Prlr"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Gpr55-Prlr-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Gpr55", "Cnr1"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Gpr55-Cnr1-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Gpr55", "Th"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Gpr55-Th-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Plot_Density_Joint_Only(
  seurat_object = onecut3,
  features = c("Gpr55", "Onecut3"),
  custom_palette = onecut3@misc$div_Colour_Pal
)

Past versions of plt-init-umap-density-Gpr55-Onecut3-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Correlation analysis visualisation between different genes

p_corrs <- list(
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    x = Onecut3,
    y = Cnr1,
    xfill = "#ffc400",
    yfill = "#e22ee2"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    x = Slc32a1,
    y = Onecut3,
    xfill = "#0000da",
    yfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    x = Gpr55,
    y = Onecut3,
    xfill = "#006eff",
    yfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    x = Slc32a1,
    y = Cnr1,
    xfill = "#0000da",
    yfill = "#e22ee2"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    x = Gpr55,
    y = Cnr1,
    xfill = "#006eff",
    yfill = "#e22ee2"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    x = Slc32a1,
    y = Gpr55,
    xfill = "#0000da",
    yfill = "#006eff"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Slc32a1,
    x = Onecut3,
    yfill = "#0000da",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Gpr55,
    x = Onecut3,
    yfill = "#006eff",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Th,
    x = Onecut3,
    yfill = "#ff0000",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Gad1,
    x = Onecut3,
    yfill = "#a50202",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Gad2,
    x = Onecut3,
    yfill = "#4002a5",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Onecut2,
    x = Onecut3,
    yfill = "#6402a5",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Prlr,
    x = Onecut3,
    yfill = "#2502a5",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Ddc,
    x = Onecut3,
    yfill = "#4002a5",
    xfill = "#ffc400"
  ),
  ggstatsplot::ggscatterstats(
    as.data.frame(mtx_oc3),
    y = Slc6a3,
    x = Onecut3,
    yfill = "#2502a5",
    xfill = "#ffc400"
  )
)
n_corrs <- list(
  "oc3-rna-data-Onecut3-Cnr1",
  "oc3-rna-data-Slc32a1-Onecut3",
  "oc3-rna-data-Gpr55-Onecut3",
  "oc3-rna-data-Slc32a1-Cnr1",
  "oc3-rna-data-Gpr55-Cnr1",
  "oc3-rna-data-Slc32a1-Gpr55",
  "oc3-rna-data-Onecut3-Slc32a1",
  "oc3-rna-data-Onecut3-Gpr55",
  "oc3-rna-data-Onecut3-Th",
  "oc3-rna-data-Onecut3-Gad1",
  "oc3-rna-data-Onecut3-Gad2",
  "oc3-rna-data-Onecut3-Onecut2",
  "oc3-rna-data-Onecut3-Prlr",
  "oc3-rna-data-Onecut3-Ddc",
  "oc3-rna-data-Onecut3-Slc6a3"
)

walk2(n_corrs, p_corrs, save_my_plot, type = "stat-corr-plt")

Visualise intersections sets that we are going to use (highlighted)

upset(
  as.data.frame(content_mtx_oc3),
  order.by = "freq",
  sets.x.label = "Number of cells",
  text.scale = c(2, 1.6, 2, 1.3, 2, 3),
  nsets = 15,
  sets = c("Th", "Onecut3"),
  queries = list(
    list(
      query = intersects,
      params = list("Onecut3"),
      active = T
    ),
    list(
      query = intersects,
      params = list("Th"),
      active = T
    ),
    list(
      query = intersects,
      params = list("Th", "Onecut3"),
      active = T
    )
  ),
  nintersects = 60,
  empty.intersections = "on"
)

Past versions of plot-upset-oc3-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

upset(
  as.data.frame(content_mtx_oc3),
  order.by = "freq",
  sets.x.label = "Number of cells",
  text.scale = c(2, 1.6, 2, 1.3, 2, 3),
  nsets = 15,
  sets = c("Gpr55", "Cnr1", "Slc32a1", "Th"),
  queries = list(
    list(
      query = intersects,
      params = list("Gpr55", "Slc32a1"),
      active = T
    ),
    list(
      query = intersects,
      params = list("Cnr1", "Th"),
      active = T
    )
  ),
  nintersects = 60,
  empty.intersections = "on"
)

Past versions of plot-upset-oc3-mod-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Regroup factor by stages for more balanced groups

onecut3$age %>% forcats::fct_count()

onecut3$stage <-
  onecut3$age %>%
  forcats::fct_collapse(
    `Embrionic day 15` = "E15",
    `Embrionic day 17` = "E17",
    Neonatal = c("P00", "P02"),
    Postnatal = c("P10", "P23")
  )
onecut3$stage %>% forcats::fct_count()

Make subset of stable neurons

onecut3$gaba_status <-
  content_mtx_oc3 %>%
  select(Gad1, Gad2, Slc32a1) %>%
  mutate(gaba = if_all(.fns = ~ .x > 0)) %>%
  .$gaba

onecut3$gaba_occurs <-
  content_mtx_oc3 %>%
  select(Gad1, Gad2, Slc32a1) %>%
  mutate(gaba = if_any(.fns = ~ .x > 0)) %>%
  .$gaba

onecut3$th_status <-
  content_mtx_oc3 %>%
  select(Th, Ddc, Slc6a3) %>%
  mutate(dopamin = if_any(.fns = ~ .x > 0)) %>%
  .$dopamin

oc3_fin <- onecut3

Check contingency tables for neurotransmitter signature

oc3_fin@meta.data %>%
  janitor::tabyl(th_status, gaba_status)

By age

oc3_fin@meta.data %>%
  janitor::tabyl(age, th_status)

By stage

oc3_fin@meta.data %>%
  janitor::tabyl(stage, th_status)

Make splits of neurons by neurotransmitter signature

oc3_fin$status <- oc3_fin$th_status %>%
  if_else(true = "dopaminergic",
    false = "GABAergic"
  )
Idents(oc3_fin) <- "status"
SaveH5Seurat(
  object    = oc3_fin,
  filename  = here(data_dir, "oc3_fin"),
  overwrite = TRUE,
  verbose   = TRUE
)

## Split on basis of neurotrans and test for difference
oc3_fin_neurotrans <- SplitObject(oc3_fin, split.by = "status")

## Split on basis of age and test for difference
oc3_fin_ages <- SplitObject(oc3_fin, split.by = "age")

DotPlots grouped by age

Expression of GABA receptors in GABAergic Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$GABAergic,
  features = gabar,
  group.by = "age",
  cols = c("#adffff", "#0084ff"),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-age-gabar-gaba-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of GABA receptors in dopaminergic TIDA or Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$dopaminergic,
  features = gabar,
  group.by = "age",
  split.by = "celltype",
  cols = list(c("#fcc2c2", "#ff3c00"), c("#fffef1", "#00FE00")),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-age-gabar-dop-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of glutamate receptors in GABAergic Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$GABAergic,
  features = glutr,
  group.by = "age",
  cols = c("#adffff", "#0084ff"),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-age-glur-gaba-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of glutamate receptors in dopaminergic TIDA or Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$dopaminergic,
  features = glutr,
  group.by = "age",
  split.by = "celltype",
  cols = list(c("#fcc2c2", "#ff3c00"), c("#fffef1", "#00FE00")),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-age-glur-dop-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

DotPlots grouped by stage

Expression of GABA receptors in GABAergic Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$GABAergic,
  features = gabar,
  group.by = "stage",
  cols = c("#adffff", "#0084ff"),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-gabar-gaba-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of GABA receptors in dopaminergic TIDA or Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$dopaminergic,
  features = gabar,
  group.by = "stage",
  split.by = "celltype",
  cols = list(c("#fcc2c2", "#ff3c00"), c("#fffef1", "#00FE00")),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-gabar-dop-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of glutamate receptors in GABAergic Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$GABAergic,
  features = glutr,
  group.by = "stage",
  cols = c("#adffff", "#0084ff"),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-glur-gaba-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of glutamate receptors in dopaminergic TIDA or Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$dopaminergic,
  features = glutr,
  group.by = "stage",
  split.by = "celltype",
  cols = list(c("#fcc2c2", "#ff3c00"), c("#fffef1", "#00FE00")),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-glur-dop-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of neuromodulators receptors in GABAergic Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$GABAergic,
  features = npr,
  group.by = "stage",
  cols = c("#adffff", "#0084ff"),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-npr-gaba-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of neuromodulators receptors in dopaminergic TIDA or Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$dopaminergic,
  features = npr,
  group.by = "stage",
  split.by = "celltype",
  cols = list(c("#fcc2c2", "#ff3c00"), c("#fffef1", "#00FE00")),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-npr-dop-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of endocannabinoids relevant genes in GABAergic Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$GABAergic,
  features = cnbn,
  group.by = "stage",
  cols = c("#adffff", "#0084ff"),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-cnbn-gaba-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Expression of endocannabinoids relevant genes in dopaminergic TIDA or Onecut3 positive cells

DotPlot(
  object = oc3_fin_neurotrans$dopaminergic,
  features = cnbn,
  group.by = "stage",
  split.by = "celltype",
  cols = list(c("#fcc2c2", "#ff3c00"), c("#fffef1", "#00FE00")),
  col.min = -1, col.max = 1
) + RotatedAxis()

Past versions of plot-dotplot-stage-cnbn-dop-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

Overrepresentation analysis

Idents(oc3_fin) <- "status"

sbs_mtx_oc <-
  oc3_fin %>%
  GetAssayData("data", "RNA") %>%
  as.data.frame() %>%
  t()
rownames(sbs_mtx_oc) <- colnames(oc3_fin)

# Filter features
filt_low_genes2 <-
  colSums(sbs_mtx_oc) %>%
  .[. > quantile(., 0.4)] %>%
  names()
sbs_mtx_oc %<>% .[, filt_low_genes2]

min_filt_vector2 <-
  sbs_mtx_oc %>%
  as_tibble() %>%
  select(all_of(filt_low_genes2)) %>%
  summarise(across(.fns = ~ quantile(.x, .005))) %>%
  as.list() %>%
  map(as.double) %>%
  simplify() %>%
  .[filt_low_genes2]

# Prepare table of intersection sets analysis
content_sbs_mtx_oc <-
  (sbs_mtx_oc > min_filt_vector2) %>%
  as_tibble() %>%
  mutate_all(as.numeric)

upset(
  as.data.frame(content_sbs_mtx_oc),
  order.by = "freq",
  sets.x.label = "Number of cells",
  text.scale = c(2, 1.6, 2, 1.3, 2, 3),
  nsets = 15,
  sets = c(
    "Th", "Onecut3",
    cnbn, "Prlr"
  ) %>%
    .[. %in% colnames(content_sbs_mtx_oc)],
  nintersects = 20,
  empty.intersections = NULL
)

Past versions of plot-upset-sbs-oc3-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

upset(
  as.data.frame(content_sbs_mtx_oc),
  order.by = "freq",
  sets.x.label = "Number of cells",
  text.scale = c(2, 1.6, 2, 1.3, 2, 3),
  nsets = 15,
  sets = c("Cnr1", "Prlr", "Th", "Onecut3") %>%
    .[. %in% colnames(content_sbs_mtx_oc)],
  nintersects = 10,
  empty.intersections = NULL
)

Past versions of plot-upset-sbs-oc3-mod-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

sbs_mtx_oc_full <- content_sbs_mtx_oc |>
  select(any_of(c(
    neurotrans, cnbn, "Prlr", "Cnr1", "Gpr55", "Onecut3"
  ))) |>
  dplyr::bind_cols(oc3_fin@meta.data)

sbs_mtx_oc_full |> glimpse()

Rows: 401
Columns: 44
$ Slc17a8          <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Slc1a1           <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,…
$ Slc1a2           <dbl> 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0,…
$ Slc1a6           <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Gad1             <dbl> 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1,…
$ Slc32a1          <dbl> 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0,…
$ Slc6a1           <dbl> 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0,…
$ Cnr1             <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,…
$ Gpr55            <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Dagla            <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,…
$ Daglb            <dbl> 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Mgll             <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Faah             <dbl> 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1,…
$ Napepld          <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Gde1             <dbl> 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1,…
$ Pparg            <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ Prlr             <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
$ Onecut3          <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
$ nGene            <int> 3034, 2551, 2029, 1415, 1513, 1079, 3160, 3072, 2778,…
$ nUMI             <dbl> 6868, 5316, 3696, 2667, 2490, 1789, 8247, 8544, 6478,…
$ orig.ident       <chr> "FC2P23", "FC2P23", "FC2P23", "FC2P23", "FC2P23", "FC…
$ res.0.2          <chr> "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5"…
$ res.0.4          <chr> "26", "26", "26", "26", "26", "26", "26", "26", "26",…
$ res.0.8          <chr> "31", "31", "31", "31", "31", "31", "31", "31", "31",…
$ res.1.2          <chr> "36", "36", "36", "36", "36", "36", "36", "36", "36",…
$ res.2            <chr> "37", "37", "37", "37", "37", "37", "37", "37", "37",…
$ tree.ident       <int> 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2…
$ pro_Inter        <chr> "17", "17", "17", "17", "17", "17", "17", "17", "17",…
$ pro_Enter        <chr> "17", "17", "17", "17", "17", "17", "17", "17", "17",…
$ tree_final       <fct> 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1…
$ subtree          <fct> 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1…
$ prim_walktrap    <fct> 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2…
$ umi_per_gene     <dbl> 2.263678, 2.083889, 1.821587, 1.884806, 1.645737, 1.6…
$ log_umi_per_gene <dbl> 0.3548147, 0.3188745, 0.2604499, 0.2752666, 0.2163604…
$ nCount_RNA       <dbl> 6868, 5316, 3696, 2667, 2490, 1789, 8247, 8544, 6478,…
$ nFeature_RNA     <int> 3034, 2551, 2029, 1415, 1513, 1079, 3160, 3072, 2778,…
$ wtree            <fct> 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3…
$ age              <chr> "P23", "P23", "P23", "P23", "P23", "P23", "P10", "P10…
$ celltype         <fct> Arc_TIDA, Arc_TIDA, Arc_TIDA, Arc_TIDA, Arc_TIDA, Arc…
$ stage            <fct> Postnatal, Postnatal, Postnatal, Postnatal, Postnatal…
$ gaba_status      <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE…
$ gaba_occurs      <lgl> TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRU…
$ th_status        <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…
$ status           <chr> "dopaminergic", "dopaminergic", "dopaminergic", "dopa…

sbs_mtx_oc_full$CB1R <-
  sbs_mtx_oc_full %>%
  select(Cnr1, Gpr55) %>%
  mutate(CB1R = Cnr1 > 0) %>%
  .$CB1R

sbs_mtx_oc_full$PRLR <-
  sbs_mtx_oc_full %>%
  select(Prlr) %>%
  mutate(PRLR = Prlr > 0) %>%
  .$PRLR

sbs_mtx_oc_full$oc3 <-
  (sbs_mtx_oc_full$Onecut3 > 0)

library(ggstatsplot)
# for reproducibility
set.seed(123)

# plot
grouped_ggpiestats(
  # arguments relevant for `ggpiestats()`
  data = sbs_mtx_oc_full,
  x = CB1R,
  y = oc3,
  grouping.var = status,
  perc.k = 1,
  package = "ggsci",
  palette = "category10_d3",
  # arguments relevant for `combine_plots()`
  title.text = "Cnr1 specification of onecut-driven hypothalamic neuronal lineages by Onecut3 and main neurotransmitter expression",
  caption.text = "Asterisks denote results from proportion tests; \n***: p < 0.001, ns: non-significant",
  plotgrid.args = list(nrow = 2)
)

Past versions of plot-piecharts-sbs-oc3-chisqr-1.png

Version	Author	Date
aaece06	Evgenii O. Tretiakov	2023-05-29

grouped_ggpiestats(
  # arguments relevant for `ggpiestats()`
  data = sbs_mtx_oc_full,
  x = PRLR,
  y = CB1R,
  grouping.var = status,
  perc.k = 1,
  package = "ggsci",
  palette = "category10_d3",
  # arguments relevant for `combine_plots()`
  title.text = "Prlr specification of onecut-driven PeVN or TIDA hypothalamic neuronal lineages by Cnr1 and main neurotransmitter expression",
  caption.text = "Asterisks denote results from proportion tests; \n***: p < 0.001, ns: non-significant",
  plotgrid.args = list(nrow = 2)
)

grouped_ggpiestats(
  # arguments relevant for `ggpiestats()`
  data = sbs_mtx_oc_full,
  x = PRLR,
  y = CB1R,
  grouping.var = celltype,
  perc.k = 1,
  package = "ggsci",
  palette = "category10_d3",
  # arguments relevant for `combine_plots()`
  title.text = "Prlr specification of onecut-driven PeVN or TIDA hypothalamic neuronal lineages by Cnr1",
  caption.text = "Asterisks denote results from proportion tests; \n***: p < 0.001, ns: non-significant",
  plotgrid.args = list(nrow = 2)
)

Session information

sessionInfo()

R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggstatsplot_0.11.1.9000 Nebulosa_1.10.0         RColorBrewer_1.1-3     
 [4] patchwork_1.1.2.9000    UpSetR_1.4.0            scCustomize_1.1.1      
 [7] SeuratDisk_0.0.0.9020   SeuratWrappers_0.3.1    SeuratObject_4.1.3     
[10] Seurat_4.3.0            sctransform_0.3.5       future_1.32.0          
[13] zeallot_0.1.0           magrittr_2.0.3          lubridate_1.9.2        
[16] forcats_1.0.0           stringr_1.5.0           dplyr_1.1.2            
[19] purrr_1.0.1             readr_2.1.4             tidyr_1.3.0            
[22] tibble_3.2.1            ggplot2_3.4.2           tidyverse_2.0.0.9000   
[25] here_1.0.1              workflowr_1.7.0        

loaded via a namespace (and not attached):
  [1] fs_1.6.2                    matrixStats_0.63.0         
  [3] spatstat.sparse_3.0-1       bitops_1.0-7               
  [5] httr_1.4.5                  insight_0.19.1             
  [7] tools_4.3.0                 utf8_1.2.3                 
  [9] R6_2.5.1                    statsExpressions_1.5.0     
 [11] mgcv_1.8-42                 lazyeval_0.2.2             
 [13] uwot_0.1.14                 withr_2.5.0                
 [15] sp_1.6-0                    gridExtra_2.3              
 [17] progressr_0.13.0            textshaping_0.3.6          
 [19] cli_3.6.1                   Biobase_2.60.0             
 [21] spatstat.explore_3.1-0      sandwich_3.0-2             
 [23] prismatic_1.1.1             labeling_0.4.2             
 [25] sass_0.4.5                  mvtnorm_1.1-3              
 [27] spatstat.data_3.0-1         ggridges_0.5.4             
 [29] pbapply_1.7-0               systemfonts_1.0.4          
 [31] R.utils_2.12.2              parallelly_1.35.0          
 [33] rstudioapi_0.14             generics_0.1.3             
 [35] shape_1.4.6                 ica_1.0-3                  
 [37] spatstat.random_3.1-4       vroom_1.6.1                
 [39] Matrix_1.5-4                ggbeeswarm_0.7.1.9000      
 [41] fansi_1.0.4                 S4Vectors_0.38.0           
 [43] abind_1.4-5                 R.methodsS3_1.8.2          
 [45] lifecycle_1.0.3             whisker_0.4.1              
 [47] multcomp_1.4-23             yaml_2.3.7                 
 [49] snakecase_0.11.0            SummarizedExperiment_1.30.0
 [51] Rtsne_0.16                  paletteer_1.5.0            
 [53] grid_4.3.0                  promises_1.2.0.1           
 [55] crayon_1.5.2                miniUI_0.1.1.1             
 [57] lattice_0.21-8              cowplot_1.1.1              
 [59] pillar_1.9.0                knitr_1.42                 
 [61] GenomicRanges_1.52.0        estimability_1.4.1         
 [63] future.apply_1.10.0         codetools_0.2-19           
 [65] leiden_0.4.3                glue_1.6.2                 
 [67] getPass_0.2-2               data.table_1.14.8          
 [69] remotes_2.4.2               vctrs_0.6.2                
 [71] png_0.1-8                   gtable_0.3.3               
 [73] rematch2_2.1.2              datawizard_0.7.1           
 [75] cachem_1.0.7                ks_1.14.0                  
 [77] xfun_0.39                   mime_0.12                  
 [79] correlation_0.8.4           ggside_0.2.2               
 [81] pracma_2.4.2                coda_0.19-4                
 [83] survival_3.5-5              SingleCellExperiment_1.22.0
 [85] ellipsis_0.3.2              fitdistrplus_1.1-11        
 [87] TH.data_1.1-2               ROCR_1.0-11                
 [89] nlme_3.1-162                bit64_4.0.5                
 [91] RcppAnnoy_0.0.20            GenomeInfoDb_1.36.0        
 [93] rprojroot_2.0.3             bslib_0.4.2                
 [95] irlba_2.3.5.1               vipor_0.4.5                
 [97] KernSmooth_2.23-20          colorspace_2.1-0           
 [99] BiocGenerics_0.46.0         ggrastr_1.0.1              
[101] tidyselect_1.2.0            processx_3.8.1             
[103] emmeans_1.8.5               bit_4.0.5                  
[105] compiler_4.3.0              git2r_0.32.0               
[107] hdf5r_1.3.8                 DelayedArray_0.25.0        
[109] plotly_4.10.1               bayestestR_0.13.1          
[111] scales_1.2.1                lmtest_0.9-40              
[113] callr_3.7.3                 digest_0.6.31              
[115] goftest_1.2-3               spatstat.utils_3.0-2       
[117] rmarkdown_2.21              XVector_0.40.0             
[119] htmltools_0.5.5             pkgconfig_2.0.3            
[121] MatrixGenerics_1.12.0       highr_0.10                 
[123] fastmap_1.1.1               rlang_1.1.0                
[125] GlobalOptions_0.1.2         htmlwidgets_1.6.2          
[127] shiny_1.7.4                 farver_2.1.1               
[129] jquerylib_0.1.4             zoo_1.8-12                 
[131] jsonlite_1.8.4              mclust_6.0.0               
[133] R.oo_1.25.0                 RCurl_1.98-1.12            
[135] GenomeInfoDbData_1.2.10     parameters_0.21.0          
[137] munsell_0.5.0               Rcpp_1.0.10                
[139] reticulate_1.28-9000        stringi_1.7.12             
[141] zlibbioc_1.46.0             MASS_7.3-59                
[143] plyr_1.8.8                  parallel_4.3.0             
[145] listenv_0.9.0               ggrepel_0.9.3              
[147] deldir_1.0-6                splines_4.3.0              
[149] tensor_1.5                  hms_1.1.3                  
[151] circlize_0.4.15             ps_1.7.5                   
[153] igraph_1.4.2                spatstat.geom_3.1-0        
[155] effectsize_0.8.3            reshape2_1.4.4             
[157] stats4_4.3.0                evaluate_0.20              
[159] BiocManager_1.30.20         ggprism_1.0.4              
[161] tzdb_0.3.0                  httpuv_1.6.9               
[163] MatrixModels_0.5-1          BayesFactor_0.9.12-4.4     
[165] RANN_2.6.1                  polyclip_1.10-4            
[167] scattermore_0.8             rsvd_1.0.5                 
[169] janitor_2.2.0.9000          xtable_1.8-4               
[171] later_1.3.0                 ragg_1.2.5                 
[173] viridisLite_0.4.1           beeswarm_0.4.0             
[175] IRanges_2.34.0              cluster_2.1.4              
[177] timechange_0.2.0            globals_0.16.2