query_biomart.Rmd

#### BiomaRt Biotype Analysis

See BioMartR documentation [here](https://cran.r-project.org/web/packages/biomartr/vignettes/Functional_Annotation.html)

Load ensembl db annotation.

```{r}
# load ensembl 
ensembl <- useEnsembl(
  biomart = "genes", 
  dataset = "hsapiens_gene_ensembl"
  )
```

retrieve annotation for select proteins.

```{r}
mapping <- getBM(
  attributes = c(
    'ensembl_gene_id', 
    #'ensembl_transcript_id',
    'hgnc_symbol',
    "go_id", "namespace_1003", "name_1006"), 
  filters = 'hgnc_symbol',
  values = my_annotation$EntrezGeneSymbol %>% unique,
  mart = ensembl
)
# map
mapping
```

Sort Biomart Annotation and filter for the three most common terms.

```{r}
# sort and filter
mapping %>% 
  # look for biological processes only
  dplyr::filter(namespace_1003 == "biological_process") %>% 
  dplyr::group_by(name_1006) %>%
  dplyr::tally() %>%
  dplyr::arrange(dplyr::desc(n)) %>%
  dplyr::slice_head(n=40) %>%
  dplyr::pull(name_1006) -> my_terms
# print out
glue::glue("my_terms are:\t{my_terms}")
# filter table
mapping %>%
  dplyr::filter(namespace_1003 == "biological_process", name_1006 %in% my_terms) -> placeholder
# 
placeholder %>%
  dplyr::select(hgnc_symbol, name_1006) %>%
  dplyr::mutate(value = 1) %>%
  tidyr::pivot_wider(names_from=name_1006, values_fn=min ) -> my_biomart

my_biomart %>%
  as.data.frame -> my_biomart_df
rownames(my_biomart_df) <- my_biomart_df$hgnc_symbol
# replace NA with 0
my_biomart_df[is.na(my_biomart_df)] <- 0

```

set color code for heatmap

```{r}
# set minimum
min_val <- -10
# set max
max_val <- +10
# Sets the minimum (0), the maximum (15), and the increasing steps (+1) for the color scale
# Note: if some of your genes are outside of this range, they will appear white on the heatmap
breaksList = seq(min_val, max_val, by = 0.1)
# Defines the vector of colors for the legend (it has to be of the same lenght of breaksList)
color_code = colorRampPalette(c("blue", "white", "red"))(length(breaksList))
```

make pheatmap

```{r, eval=FALSE}
# create categorical color vector for terms
color_vctr <- c( "N" = "white", "Y" = "red")
annoCol <- rep(list(color_vctr), 10)
names(annoCol) <- my_terms
# draw heatmap
pheatmap::pheatmap(
  my_matrix, 
  scale="row", 
  cluster_rows=T, 
  cluster_cols=T,
  show_colnames=FALSE,
  color=color_code, 
  breaks=breaksList, 
  cellwidth=3, 
  cellheight=5,
  fontsize_row=4,
  fontsize_col=4,
  treeheight_row=0.0,
  treeheight_col=0.0,
  annotation_row = my_biomart_df %>% dplyr::select(-hgnc_symbol),
  annotation_col = my_metadata %>% dplyr::select(ARMCD),
  annotation_colors = annoCol,
  annotation_names_row=TRUE,
  annotation_legend=FALSE,
#  annotation_row=my_annotation %>% dplyr::select(EntrezGeneSymbol),
  filename=fs::path(output_img, "hm_common.png"),
  #width = 5,
  #height = 5
  )
```