README.rmd

---
title: "README"
author: "Rasmus Kirkegaard"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: github_document
always_allow_html: true
---



```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(scipen = 10)
```

```{r echo=FALSE,warning=FALSE,message=FALSE}
library(readxl)
library(kableExtra)
library(tidyverse)
d<-read_xlsx("data_links.xlsx")
```

<img align="right" src="images/microbench.jpg" width="200">

# MicroBench 

Overview of our data for microbial genomic benchmarking. We have sequenced a bunch of mono cultures, and metagenomic samples.

Monocultures:

```{r echo=FALSE,message=FALSE,results='asis'}
list_samples <- function(df) {
  # Assuming 'Sample' column contains the monoculture names
  samples <- unique(df$Sample) 

  for (sample in samples) {
    sample_formatted<-sample %>% gsub(pattern=" ",replacement="-") %>% tolower()
    cat(paste0(" * [",sample,"](#",sample_formatted,")"),"\n")
  }
}
list_samples(d %>% filter(SampleType=="monoculture"))
```

Mock Metagenomes:

```{r echo=FALSE,message=FALSE,results='asis'}
list_samples(d %>% filter(SampleType=="mock"))
```

"Real" metagenomes:

```{r echo=FALSE,message=FALSE,results='asis'}
list_samples(d %>% filter(SampleType=="metagenome"))
```

## To do:

 * Sequence all standards
 * Get AAU to support public links or upload data to NCBI/ENA

## Mono cultures

```{r echo=FALSE,message=FALSE,results='asis'}
generate_monoculture_report <- function(df) {
  # Assuming 'Sample' column contains the monoculture names
  monocultures <- unique(df$Sample) 

  for (culture in monocultures) {
    # Extract relevant information for the current monoculture
    culture_data <- df %>% 
      filter(Sample == culture) %>%
      arrange(desc(`date of basecalling`))

    # Create the markdown output
    cat("###", culture, "\n\n")  # Heading with culture name

    # Construct the DSMZ link (assuming a pattern in your data)
    dsmz_link <- culture_data$SampleInfo[1]
    
    cat("You find a description of this sample here: [",dsmz_link,"](",dsmz_link,")\n")

    # Output the table
    print(culture_data %>% select(-c(	SampleType,SampleInfo)) %>% 
            mutate(fast = case_when(is.na(fast)~NA,
                           TRUE~cell_spec("fast", "html", link = fast))) %>%
            mutate(hac = case_when(is.na(hac)~NA,
                           TRUE~cell_spec("hac", "html", link = hac))) %>%
            mutate(sup = case_when(is.na(sup)~NA,
                           TRUE~cell_spec("sup", "html", link = sup))) %>%
            mutate(hacdup = case_when(is.na(hacdup)~NA,
                           TRUE~cell_spec("hacdup", "html", link = hacdup))) %>%
            mutate(supdup = case_when(is.na(supdup)~NA,
                           TRUE~cell_spec("supdup", "html", link = supdup))) %>%
            mutate(mods = case_when(is.na(mods)~NA,
                           TRUE~cell_spec("mods", "html", link = mods))) %>%
            mutate(pod5 = case_when(is.na(pod5)~NA,
                           TRUE~cell_spec("pod5", "html", link = pod5))) %>%
            kable(format="html",escape = F) %>%
    kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive" ,"bordered"), 
                  full_width=FALSE,  position = "left"))
    cat("\n\n")
  }
}
generate_monoculture_report(d %>% filter(SampleType=="monoculture"))
```

## Mock metagenomes

```{r echo=FALSE,message=FALSE,results='asis'}
generate_monoculture_report(d %>% filter(SampleType=="mock"))
```

## "Real" metagenomes

```{r echo=FALSE,message=FALSE,results='asis'}
generate_monoculture_report(d %>% filter(SampleType=="metagenome"))
```