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42-G42.rmd
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# IGHV4-59 - G42
```{r}
source("functions.R")
```
```{r, echo=FALSE}
load("data.rda")
chain = "IGH"
func <- data.frame(allele = names(vgerms[[chain]]), functionality = !grepl("(ORF|P)",sapply(seqinr::getAnnot(vgerms_full[[chain]]), function(x) unlist(strsplit(x,"[|]"))[4])), sign = sapply(seqinr::getAnnot(vgerms_full[[chain]]), function(x) unlist(strsplit(x,"[|]"))[4]), stringsAsFactors = F)
mat <- mat_list$IGH$functional$nonsingle$all$`318`
load("data_frac_new2.rda")
data <- setDT(data_frac$IGH$functional$nonsingle$all$`318`$complete$`95`)
data[,v_call:=paste0(v_gene,"*",v_allele)]
load("alleles_dbs.rda")
allele_db <- alleles_dbs$IGH$functional$nonsingle$all$`318`$complete$`95`
allele_db <- allele_db %>% dplyr::rowwise() %>% dplyr::mutate(gene = alakazam::getGene(or_allele, strip_d = F, omit_nl = F), group = strsplit(gsub(gene, "", new_allele),"[*]")[[1]][1], gene_group = alakazam::getGene(new_allele, strip_d = F, omit_nl = F))
load("functional_groups.rda")
func_groups <- functional_groups$IGH$functional$nonsingle$all$`318`$complete$`95`
cols <- c("#FAAB18", "#1380A1","#990000", "#588300")
pal <- cols %>%
newpal(names = c("orangy", "bluish", "redish", "greeny"))
edit_links <- readLines("edit_links.txt")
share_links <- readLines("share_links.txt")
```
```{r,echo=FALSE}
g_group = "IGHV4-59G42"
group = names(func_groups)[func_groups==g_group]
gr <- allele_db %>% filter(gene_group == g_group) %>% pull(group) %>% unique()
g <- allele_db %>% filter(gene_group == g_group) %>% pull(gene) %>% unique()
```
## Allele appearnce
The group of `r group` includes `r length(grep(g_group,allele_db$new_allele,value=T))` alleles, `r sum(func$functionality[func$allele %in% allele_db$or_allele[grep(g_group,allele_db$new_allele)]])` out of the alleles are functional.
No rearrangments were found for this group, hence the general summary statistics do not apply here and were omitted.
## Observations
This section is editable by clicking on the edit button below. To refresh the section click on the refresh button
You can access the file also from [here](`r edit_links[grep(g_group,edit_links)]`){target="_blank"}
```{r, message=F, echo=F, warning=F}
knitr::include_url(paste0("https://peresay.shinyapps.io/G2_group/?group=",g_group))
# # Authenticate and save token for later use2
# token <- drop_auth(rdstoken = "dropbox_token.rds")
#
# # Retrieveing your file is as simple as
# drop_download("public/conclusions/IGHV1-2.docx", local_path = "docs/IGHV1-2.docx",
# overwrite = TRUE, verbose = FALSE, progress = FALSE)
# drop_df <- textreadr::read_docx("docs/IGHV1-2.docx")
# invisible(rmarkdown::pandoc_convert(input = "IGHV1-2.docx", to = "markdown", output = "IGHV1-2_docx.md", options = c("--wrap=none","--reference-links","--metadata-file=metadata.yaml","--standalone"), wd = "docs", verbose = FALSE))
#
# ui <- fluidPage(
#
# # Application title
# mainPanel(
# shiny::actionButton(inputId='ab1', label="Edit text",
# icon = icon("edit"),
# onclick ="window.open('https://www.dropbox.com/scl/fi/crphl3u49fmkw8wnb5v71/IGHV1-2.docx?dl=0&rlkey=l54oqhrlxx8wyp6bywr224sx0')"),
#
# shiny::actionButton(inputId='ab2', label="Reload text",
# icon = icon("sync-alt")),
#
# #htmlOutput("df_output"),
# uiOutput('markdown')
# )
# )
#
# server <- function(input, output) {
#
# observeEvent(input$ab2, {
# drop_download("public/conclusions/IGHV1-2.docx", local_path = "docs/IGHV1-2.docx",
# overwrite = TRUE, verbose = F)
# #drop_df <- textreadr::read_docx("docs/IGHV1-2.docx")
#
# rmarkdown::pandoc_convert(input = "IGHV1-2.docx", to = "markdown", output = "IGHV1-2_docx.md", options = c("--wrap=none","--reference-links","--metadata-file=metadata.yaml","--standalone"), wd = "docs", verbose = F)
# output$markdown <- renderUI({
# #withMathJax(includeMarkdown(knitr::knit('IGHV1-2_docx.md', quiet = TRUE)))
# HTML(markdown::markdownToHTML(knitr::knit('docs/IGHV1-2_docx.md', quiet = TRUE)))
# })
#
# })
#
# # output$df_output <- renderUI({
# # if(input$ab2) return()
# # HTML(paste(drop_df, collapse = "<br/><br/>"))
# # })
#
# output$markdown <- renderUI({
# #withMathJax(includeMarkdown(knitr::knit('docs/IGHV1-2_docx.md', quiet = TRUE)))
# HTML(markdown::markdownToHTML(knitr::knit('docs/IGHV1-2_docx.md', quiet = TRUE)))
# })
# }
#
# shinyApp(ui = ui, server = server)
```
## Conclusions