4b.Rmd

---
title: "Figure 4"
output:
  html_document:
    df_print: paged
---

### To enable free text search and generate wordcloud from the result, users need to download the `freetext` version of `scfind`
```{r message=FALSE, warning=FALSE} 
devtools::install_github(repo = "hemberg-lab/scfind",
                         ref = "freetext",
                         force = T # In case user already installed scfind 3.5.0 version
                         )
library("scfind")
```

### Figure 4
```{r eval=FALSE, message=FALSE, warning=FALSE, include=FALSE, paged.print=TRUE}
object <- loadObject(url("https://scfind.cog.sanger.ac.uk/indexes/tm_facs.rds"))

download.file(url = ("https://scfind.cog.sanger.ac.uk/w2v/scfind_dictionary_mm_v1.rds"),
              destfile = "data/dictionary.rds", 
              method="curl")

download.file(url = ("http://evexdb.org/pmresources/vec-space-models/PubMed-w2v.bin"),
              destfile = "data/w2v.bin", 
              method="curl")

dictionary <- scfindQ2loadDictionaries(w2v = "data/w2v.bin", dictionary = "data/dictionary.rds")
scfindShiny(dictionary = dictionary, object = object)

```

# Input the following arbitrary query for result:

### factor xa
### Irx4, Myl2, Xdh, Dlk1, Hyal2, Tmem190, Cpne4, Cyp1a1 and Irx5
### endurance capacity for marathon Col5a1 rs12722