Lakhansing Pardeshi
July 20, 2025
Metadata for all the genome in the current pangenome along with carotovoricin presence/absence information
geNomad prophage prediction result summary for 454 genomes
Prophage clustering based on syntenic Jaccard index
Carotovoricin cluster presence/absence data
Carotovoricin cluster homology groups and their functional categories
Homology group based haplotypes for the tail fiber locus
---
title: "Supplementary tables for carotovoricin analysis"
author: "Lakhansing Pardeshi"
date: "`r Sys.Date()`"
format:
html:
embed-resources: true
df-print: paged
knitr:
opts_chunk:
fig.height: 7
---
```{r}
#| label: setup
#| echo: false
#| warning: false
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(org.Pectobacterium.spp.pan.eg.db))
suppressPackageStartupMessages(library(DT))
suppressPackageStartupMessages(library(openxlsx))
rm(list = ls())
source("https://raw.githubusercontent.com/lakhanp1/omics_utils/main/RScripts/utils.R")
source("scripts/utils/config_functions.R")
source("scripts/utils/homology_groups.R")
################################################################################
set.seed(124)
confs <- prefix_config_paths(
conf = suppressWarnings(configr::read.config(file = "project_config.yaml")),
dir = "."
)
pangenome <- confs$data$pangenomes$pectobacterium.v2$name
panConf <- confs$data$pangenomes[[pangenome]]
panOrgDb <- org.Pectobacterium.spp.pan.eg.db
```
```{r}
#| echo: false
#| warning: false
## write tables to excel file
wb <- openxlsx::createWorkbook()
add_table_to_workbook <- function(data, wb, table_num, description = "## Table"){
currentSheet <- paste("Table_S", table_num, sep = "")
openxlsx::addWorksheet(wb, sheetName = currentSheet)
openxlsx::writeData(
wb = wb, sheet = currentSheet,
x = description
)
openxlsx::writeDataTable(
wb = wb, x = data, sheet = currentSheet,
startCol = 1, startRow = 2, withFilter = TRUE,
keepNA = TRUE, na.string = "NA"
)
openxlsx::freezePane(wb = wb, sheet = currentSheet, firstActiveRow = 3, firstActiveCol = 2)
return(wb)
}
table_counter <- 1
```
::: {.panel-tabset}
## Table S`r table_counter`
Metadata for all the genome in the current pangenome along with carotovoricin presence/absence information
```{r}
#| echo: false
#| column: screen-inset-right
metadata <- suppressMessages(readr::read_csv(panConf$files$metadata)) %>%
dplyr::select(-starts_with("nodepath."), -Genome) %>%
dplyr::select(
genomeId, SpeciesName, sampleId, strain, AssemblyAccession, geo_loc_country, collection_year,
host, env_broad_scale, type_material, AssemblyName, BioprojectAccn,
BioSampleAccn, length, N50, L50, n_contigs
)
wb <- add_table_to_workbook(
data = metadata, wb = wb, table_num = table_counter,
description = paste(
"## Table S", table_counter, ": Metadata for genome assemblies used in the current pangenome",
sep = ""
)
)
DT::datatable(
data = metadata,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
table_counter <- table_counter + 1
```
## Table S`r table_counter`
geNomad prophage prediction result summary for 454 genomes
```{r}
#| echo: false
#| column: screen-inset-right
prophages <- suppressMessages(readr::read_tsv(confs$data$prophages$files$data)) %>%
dplyr::mutate(
integrated = dplyr::if_else(
condition = is.na(start) & is.na(end), true = "N", false = "Y"
)
) %>%
dplyr::select(prophage_id, genomeId, everything()) %>%
dplyr::relocate(integrated, .after = end) %>%
dplyr::left_join(
y = dplyr::select(metadata, genomeId, strain),
by = "genomeId"
) %>%
dplyr::relocate(strain, .after = SpeciesName)
wb <- add_table_to_workbook(
data = prophages, wb = wb, table_num = table_counter,
description = paste(
"## Table S", table_counter, ": geNomad prophage prediction result summary for 454 genomes",
sep = ""
)
)
DT::datatable(
data = prophages,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
table_counter <- table_counter + 1
```
## Table S`r table_counter`
Prophage clustering based on syntenic Jaccard index
```{r}
#| echo: false
#| column: screen-inset-right
phage_grps <- suppressMessages(
readr::read_tsv(confs$analysis$prophages$files$clusters)
) %>%
dplyr::select(-starts_with("nodepath.")) %>%
dplyr::left_join(
y = dplyr::select(metadata, genomeId, strain),
by = "genomeId"
) %>%
dplyr::relocate(strain, .after = SpeciesName)
wb <- add_table_to_workbook(
data = phage_grps, wb = wb, table_num = table_counter,
description = paste(
"## Table S", table_counter, ": Prophage clustering based on syntenic Jaccard index",
sep = ""
)
)
DT::datatable(
data = phage_grps,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
table_counter <- table_counter + 1
```
## Table S`r table_counter`
Carotovoricin cluster presence/absence data
```{r}
#| echo: false
#| column: screen-inset-right
ctvPav <- suppressMessages(
readr::read_tsv(file = confs$analysis$ctv$data$files$ctv_pav)
) |>
dplyr::rename(
"n_homology_groups" = nHgs,
"homology_group_signature" = hgs,
"coordinates" = pos
)
wb <- add_table_to_workbook(
data = ctvPav, wb = wb, table_num = table_counter,
description = paste(
"## Table S", table_counter, ": Carotovoricin presence.absence data for 454 genomes.",
"In case of carotovoricin cluster split onto multiple contigs, \"|\" seperator is used for coordinates and homology_group_signature columns",
sep = ""
)
)
DT::datatable(
data = ctvPav,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 2),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
table_counter <- table_counter + 1
```
## Table S`r table_counter`
Carotovoricin cluster homology groups and their functional categories
```{r}
#| echo: false
#| column: screen-inset-right
ctvHgs <- suppressMessages(
readr::read_tsv(file = confs$analysis$ctv$data$files$hg_broad_functions)
) |>
dplyr::rename(homology_group = hgId)
wb <- add_table_to_workbook(
data = ctvHgs, wb = wb, table_num = table_counter,
description = paste(
"## Table S", table_counter, ": Carotovoricin cluster homology groups and their functional categories",
sep = ""
)
)
DT::datatable(
data = ctvHgs,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 3),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
table_counter <- table_counter + 1
```
## Table S`r table_counter`
Homology group based haplotypes for the tail fiber locus
```{r}
#| echo: false
#| column: screen-inset-right
tfl_haplotypes <- suppressMessages(
readr::read_tsv(file = confs$analysis$ctv$tfl$files$hg_regions)
) |>
dplyr::add_count(haplotype, name = "n") |>
dplyr::rename(
"n_homology_groups" = nHgs,
"homology_group_signature" = hgs
)
wb <- add_table_to_workbook(
data = tfl_haplotypes, wb = wb, table_num = table_counter,
description = paste(
"## Table S", table_counter, ": Carotovoricin tail fiber locus haplotypes",
sep = ""
)
)
DT::datatable(
data = tfl_haplotypes,
rownames = FALSE,
filter = "top",
class = 'compact hover',
extensions = c('KeyTable', 'Scroller', 'Select', 'SearchBuilder', 'FixedColumns'),
options = list(
autoWidth = FALSE,
dom = 'Qlfrtip',
scrollX = TRUE,
fixedColumns = list(leftColumns = 3),
keys = TRUE,
scroller = TRUE,
scrollY = 600
),
selection = 'none'
)
table_counter <- table_counter + 1
```
:::
```{r}
#| echo: false
# save all table to Excel file
openxlsx::saveWorkbook(
wb = wb, overwrite = TRUE,
file = file.path("reports/manuscript_ctv", "ms_ctv_supplementary_data.xlsx")
)
```