Skip to content

Commit

Permalink
cleaned report layout
Browse files Browse the repository at this point in the history
  • Loading branch information
@ayeletperes
ayeletperes committed Apr 16, 2024
1 parent 486e7b8 commit a0d8ec9
Show file tree
Hide file tree
Showing 2 changed files with 68 additions and 55 deletions.
68 changes: 34 additions & 34 deletions R/ui_edit.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,40 +2,40 @@
NULL

# @export
# addTrafficLighting <- function(vector_of_colours){
# css_file = file("results/repcred.css")
#
# div_main_css = "#div-main {
# position:fixed;
# top: calc(35%);
# left: calc(35%);
# }"
#
# shiny_notif_css = ".shiny-notification {
# position:fixed;
# top: calc(55%);
# left: calc(35%);
# width: 300px;
# }"
# line_list <- vector("character" , length(vector_of_colours)+2)
# line_list[1] = div_main_css
# line_list[2] = shiny_notif_css
# i=1
#
# for(color in vector_of_colours){
# single_element_css = paste("li.chapter",as.character(i),"{",
# "background:",as.character(color),";",
# "}"
# ,sep="")
#
# line_list[i+2] = single_element_css
# i=i+1
#
# }
# writeLines(line_list,css_file)
# close(css_file)
#
# }
addTrafficLighting <- function(vector_of_colours){
css_file = file("results/repcred.css")

div_main_css = "#div-main {
position:fixed;
top: calc(35%);
left: calc(35%);
}"

shiny_notif_css = ".shiny-notification {
position:fixed;
top: calc(55%);
left: calc(35%);
width: 300px;
}"
line_list <- vector("character" , length(vector_of_colours)+2)
line_list[1] = div_main_css
line_list[2] = shiny_notif_css
i=1

for(color in vector_of_colours){
single_element_css = paste("li.chapter",as.character(i),"{",
"background:",as.character(color),";",
"}"
,sep="")

line_list[i+2] = single_element_css
i=i+1

}
writeLines(line_list,css_file)
close(css_file)

}

#'
#'
Expand Down
55 changes: 34 additions & 21 deletions inst/rstudio/templates/project/project_files/index.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -118,60 +118,72 @@ if (!is_compliant) {
missing_columns <- findMissingColumns(repertoire)
if (length(missing_columns) > 0) {
writeLines("<h3> Columns with missing / No data </h3> ")
kbl(data.table(column_name = missing_columns))
#kbl(data.table(column_name = missing_columns))
writeLines(paste0(missing_columns, collapse = ","))
}
```


# Non-nucleotides in sequence

```{r warning=FALSE}
```{r check_nucleotides, warning=FALSE}
#SECTION 3
check_nucleotides(repertoire) # TODO: this works only on the sequence column. If missing, should it be changed to sequence_alignment?
```

# Statistics
This section provides useful statistics about the repertoire:

```{r}
```{r productive_info}
repertoire$productive <- as.logical(repertoire$productive)
non_prod <- F
if(any(!is.na(repertoire$productive))){
prod_info <- data.table("Category"=factor(repertoire$productive,
levels = c("TRUE","FALSE")))
non_prod <- any(!repertoire$productive)
}
```

```{r vj_column_info}
vj_column <- "vj_in_frame" %in% colnames(repertoire)&!any(is.na(repertoire$vj_in_frame))
```

```{r cols_non_prod_breakdown}
cols_non_prod_breakdown <- all(c("vj_in_frame","stop_codon") %in% colnames(repertoire)) &!any(is.na(repertoire$vj_in_frame)) &!any(is.na(repertoire$stop_codon))
if(cols_non_prod_breakdown){
cols_non_prod_breakdown <- cols_non_prod_breakdown & non_prod
}
```

`r if(non_prod){"### Productive vs. non-productive sequences"}`
```{r, fig.cap= "The number of productive and non productive sequences. The x-axis is the productive definition, and the y-axis is the abdunce count.",warning=TRUE, eval=non_prod }
## Productive vs. non-productive sequences

```{r non_prod_figure, fig.cap= "The number of productive and non productive sequences. The x-axis is the productive definition, and the y-axis is the abdunce count.", warning=TRUE,results="asis"}
#SECTION 4
ggplot2::ggplot(
prod_info,
aes(x = !!as.name("Category"))) +
ggplot2::geom_bar(stat="count") +
ggpubr::theme_pubclean() +
ggplot2::labs(x = "", y = "Occurences") +
ggplot2::labs(x = "", y = "Number of sequences") +
ggplot2::scale_x_discrete(drop = FALSE, labels=c("Productive", "Non-productive", "NA/Not specified"))
```

```{r non_prod_table, warning=FALSE,results="asis"}
knitr::kable(prod_info %>%
dplyr::count(!!as.name("Category"), name = "Occurences", .drop = F) %>%
dplyr::mutate("Category" = as.character(!!as.name("Category")),
"Category" = dplyr::recode(!!as.name("Category"),"TRUE"="Productive",
"FALSE"="Non-productive"),
"Category" = tidyr::replace_na(!!as.name("Category"),"NA/Not specified")))
dplyr::count(!!as.name("Category"), name = "Number of sequences", .drop = F) %>%
dplyr::mutate("Category" = as.character(!!as.name("Category")),
"Category" = dplyr::recode(!!as.name("Category"),"TRUE"="Productive",
"FALSE"="Non-productive"),
"Category" = tidyr::replace_na(!!as.name("Category"),"NA/Not specified")))
```

`r if(vj_column){"### Percentage of sequences where the V and J region are in-frame"}`
`r if(vj_column){"## Percentage of sequences where the V and J region are in-frame"}`

```{r , eval=vj_column,comment=NA,results="asis"}
writeLines(paste0("Retrived information from the vj_in_frame column, precentage of V-J seuqences in frame: ",formatC(mean(as.logical(repertoire$vj_in_frame))*100,digits = 5),"%"))
```
`r if(cols_non_prod_breakdown){"### Non-productive sequences breakdown"}`

`r if(cols_non_prod_breakdown){"## Non-productive sequences breakdown"}`

```{r, fig.cap= "A breakdown of the type of non-productive sequences. The x-axis is the non-productive type, and the y-axis is the abdunce count. The red color represents sequences that has both a stop codon and the V-J is not in frame, gray color represents sequences that are in either types.", warning=TRUE, eval=cols_non_prod_breakdown}
### table the columns that indicate non-productive sequences.
Expand Down Expand Up @@ -219,7 +231,7 @@ knitr::kable(data.frame("Category" = c("Contains stop codons",
"stop_codon"="Contains stop codons")))
```

### Sequence length distribution
## Sequence length distribution

```{r, fig.cap="The sequences length distribution. The x-axis is the binned sequence lengths, and the y-axis is the frequency.", warning=FALSE,results="asis"}
Expand Down Expand Up @@ -252,8 +264,6 @@ knitr::kable(length_info)
```
# Annotation Calls Statistics

## Number of unique allele calls per gene

```{r calls info}
v_usage_info <- getGeneAlleleStat(repertoire, reference = germline_reference, call = "v_call")
d_usage_info <- getGeneAlleleStat(repertoire, reference = germline_reference, call = "d_call")
Expand All @@ -278,6 +288,8 @@ if(!is.null(germline_reference)) {
}
```

## Number of unique allele calls per gene

```{r fig.height=size, warning=TRUE, fig.subcap=c("Unique allele calls per gene. Each row is a different gene segment (V/D/J). The x-axis is the different genes, and the y-axis is the count."),results="asis"}
ggplot2::ggplot(appearance_info,
ggplot2::aes(x = !!as.name("gene"), y = !!as.name("count_unique_alleles"))) +
Expand All @@ -290,6 +302,7 @@ ggplot2::ggplot(appearance_info,
scales = "free") + ggplot2::coord_flip()
```

## Relative usage

```{r fig.height=size, warning=TRUE, fig.subcap=c("Gene usage. Each row is a different gene segment (V/D/J). The x-axis is the different genes, and the y-axis is the relative usage."),results="asis"}
Expand Down Expand Up @@ -385,7 +398,7 @@ ggplot2::ggplot(usage_info,

# General Sumrep Statistics

```{r warning=TRUE,results="asis"}
```{r warning=FALSE,results="asis"}
### summrep statistics graphs = hot/cold spots, GC content, Mutation and germline
Expand Down Expand Up @@ -626,7 +639,7 @@ ggplot(freq_table,aes(x=call,y=Freq,fill=sequence))+geom_bar(stat="identity")+gu

`r if(multiple_vgene){"Below contain CDR3 sequences with more than one v_call:"}`

```{r warning = TRUE, eval=multiple_vgene}
```{r cdr3_dist, warning = TRUE, eval=multiple_vgene}
options(width = 2000)
num_to_display=0
if(length(repertoire$sequence)>100000){
Expand All @@ -644,9 +657,9 @@ repcred:::plotVgeneDist(cdr3_data_table = cdr3_vcalls,
#kbl(most_chimeric)
```

```{r warning = TRUE, results="asis"}
```{r trafic_light, warning = TRUE, results="asis"}
#kbl(as.data.table(findAmplificationAreas(repertoire)))
#repcred:::addTrafficLighting(c(section_1,section_2,section_3,section_4,section_5,section_6,section_7,section_8,section_9,section_10,section_11))
repcred:::addTrafficLighting(c(section_1,section_2,section_3,section_4,section_5,section_6,section_7,section_8,section_9,section_10,section_11))
```


0 comments on commit a0d8ec9

Please sign in to comment.