assess_cell_purity.qmd

---
title: "Assess cell purities and inflammation"
author: "Aurélien Ginolhac"
date: "2024-10-22"
embed-resources: true
---

```{r}
#| label: setup
#| include: false

library(tidyverse)
library(ggbeeswarm)
```

## Markers  Astro and Micro and inflammation


```{r}
read_tsv("TPM_siNEG_3cell_types.tsv.gz", show_col_types = FALSE) |>  
  filter(gene_name %in% c(  "Ccl5", "Tnf", "Ptgs2", "Il1b", "Il6",
                           "Cxcl10", "Nos2"),
         cell != "Oligodendrocytes") |> 
  ggplot(aes(x = cell, y = value, color = sex)) +
  geom_quasirandom(dodge.width = 0.5, alpha = 0.2) +
  stat_summary(fun = "mean", geom = "point", aes(shape = "mean"),
               size = 3,
               position = position_dodge(width = 0.5)) +
  facet_wrap(vars(gene_name), scales = "free_y", ncol = 2L) +
  scale_shape_manual(values = 8) +
  scale_y_continuous(labels = scales::label_comma()) +
  theme_bw(13) +
  theme(legend.position = "top",
        axis.text.y = element_text(size = 7),
        panel.grid.minor = element_blank()) +
  guides(colour = guide_legend(override.aes = list(size = 2))) +
  labs(y = "Transcripts per million (TPM)",
       subtitle = "Condition: siNEG",
       x = NULL,
       shape = NULL,
       title = "Gene expressions from GRCm39")
```


## Marker Oligo Astro Microglia for assessing culture purity

```{r}
read_tsv("TPM_siNEG_3cell_types.tsv.gz", show_col_types = FALSE) |> 
  filter(gene_name %in% c("Olig2", "Gfap", "Aif1", "Itgam", "Ng2",
                          "Olig1", "Sox10", "Cnp", "Mag", "Mog", "Mbp")) |> 
  ggplot(aes(x = cell, y = value, color = sex)) +
  geom_quasirandom(dodge.width = 0.5, alpha = 0.2) +
  stat_summary(fun = "mean", geom = "point", aes(shape = "mean"),
               size = 3,
               position = position_dodge(width = 0.5)) +
  facet_wrap(vars(gene_name), scales = "free_y", ncol = 2L) +
  scale_shape_manual(values = 8) +
  scale_y_continuous(labels = scales::label_comma()) +
  theme_bw(13) +
  theme(legend.position = "top",
        axis.text.y = element_text(size = 7),
        axis.text.x = element_text(angle = 45, hjust = 1),
        panel.grid.minor = element_blank()) +
  guides(colour = guide_legend(override.aes = list(size = 2))) +
  labs(y = "Transcripts per million (TPM)",
       subtitle = "Condition: siNEG",
       x = NULL,
       shape = NULL,
       title = "Gene expressions from GRCm39")
```