tidybiology_viz_february_walkthrough.Rmd

---
title: "tidybiology january viz challenge"
output:
  html_document:
    df_print: paged
    toc: yes
  html_notebook:
    toc: yes
    toc_float: yes
---
Prism drug data

##Load libraries
```{r load_block, echo=TRUE, message=FALSE, warning=FALSE}
library(tidyverse)
library(lubridate)
library(here)
library(janitor)
library(beepr) #long analysis; get some coffee, and comeback when ready
#clear environment
#rm(list=ls()) 
#how long?
start_time <- Sys.time()
```

#import
These are log-fold change collapsed replicates with outliers and controls removed
```{r import}
prism_url <- "https://ndownloader.figshare.com/files/17741420" #primary-screen-replicate-collapsed-logfold-change.csv
prismmeta_url <- "https://ndownloader.figshare.com/files/20237715" #primary-screen-replicate-collapsed-treatment-info.csv

prism <- read_csv(prism_url, col_names = TRUE) %>% 
  clean_names()

prism_long <- prism %>% 
  #slice(1:10) %>% 
  pivot_longer(cols = -x1, names_to = "drug", values_to = "log2fc")

prism_meta <- read_csv(prismmeta_url, col_names = TRUE) %>% 
  clean_names()

head(prism)

head(prism_long)
```



#eda
```{r}
ggplot(prism_meta) +
  geom_histogram(aes(x = dose))

ggplot(prism_long) +
  geom_histogram(aes(x = log2fc), bins = 50)

ggplot(prism_long) +
  geom_density(aes(x = log2fc))
```

#Join the datasets

```{r join}
prism_meta_new <- prism_meta %>% 
                    mutate(drug_meta = str_to_lower(broad_id)) %>% 
                    mutate(drug_meta = str_replace_all(drug_meta, "-", "_")) 
prism_join <- prism_long %>% 
                mutate(drug_short = str_sub(drug, 1, 22)) %>% 
                left_join(prism_meta_new, by = c("drug_short" = "drug_meta")) 
```

#Make the plot

```{r plot}
prism_bigfc <- filter(prism_join, log2fc <= -2)
ggplot(prism_bigfc, aes(x=phase, y=log2fc)) +
  geom_jitter(aes(color= str_match(moa, "tubulin polymerization inhibitor")), alpha = 0.1) 
ggplot(prism_bigfc, aes(x=phase, y=log2fc)) +
  geom_jitter(aes(color= str_match(moa, "tubulin polymerization inhibitor")), alpha = 0.1) +
  scale_color_manual(values = c("darkred")) +
  guides(color = "none") +
  theme_bw() +
  labs(x = "Phase",
       title = "Rainfall Plot",
       subtitle = "Plotting Prism data",
       caption = "By: [Insert your name]")
```

#how long?
```{r}
end_time <- Sys.time()
time_taken <- round(as.duration(start_time %--% end_time)/dminutes(1), digits = 1)
print(time_taken)
```
Approximate time to run was `r time_taken` minutes.

#print Session information for provenance and reproducibility
```{r}
utils:::print.sessionInfo(sessionInfo()[-8]) 
#You can remove an item from sessionInfo(), which is a list with a class attribute, by printing the resulting object omitting one of the list items (omitted list of packages installed, but not loaded)
```
#stamp
```{r}
lubridate::stamp("Data updated December 31, 1979")(now())
```

#beep
```{r}
beep(sound = 8) #because mario is awesome
```