no_hit_query_analysis.Rmd

---
title: "no_hit_query_analysis"
output: html_document
date: "2024-11-11"
---

```{r}
library(readr)
library(ggplot2)
library(tidyverse)

query_ids <- read_table("workflow/out/blast/sample_1_0_02_ids.txt")
no_hit_query_ids <- read_table("workflow/out/blast/qseqs_no_blast_hits.txt")
seq_lengths <- read_csv("workflow/out/blast/sample_1_0_02_seqLengths.csv")
embeddings_not_in_species_map <- read_table("workflow/out/blast/embedding_not_in_species.txt")
```


```{r}
seq_lengths_hits <- seq_lengths %>%
  mutate(blast_hit = ifelse(qseqid %in% no_hit_query_ids$qseqid, 
                            "no", 
                            "yes"))

# check
nrow(subset(seq_lengths_hits, blast_hit == "no"))
nrow(subset(seq_lengths_hits, blast_hit == "yes"))
nrow(no_hit_query_ids)
nrow(query_ids)
nrow(query_ids) - nrow(no_hit_query_ids)
```


```{r}
ggplot(seq_lengths_hits, aes(y = length, x = blast_hit)) + 
  geom_boxplot()

ggplot(seq_lengths_hits, aes(x = length, color = blast_hit, fill = blast_hit)) + 
  geom_density()

ggplot(subset(seq_lengths_hits, length < 1000), aes(y = length, x = blast_hit, color = blast_hit)) + 
  geom_boxplot()

ggplot(subset(seq_lengths_hits, length < 1000), aes(x = length, color = blast_hit, fill = blast_hit)) + 
  geom_density(alpha = 0.3)
```

# node embeddings not making it into the species map
```{r}

```