OCEAN/.Rhistory at main · RobertsLab/OCEAN · GitHub

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reticulate::repl_python()
library(tidyverse)
library(DT)
library(readxl)
library(plotly)
# Base path for input files
base_path <- "../docs/jbrowse/function/"
# Load required packages
library(readr)
library(DT)
# Read the CSV file
nr_data <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/nr.csv")  # If running in RStudio, adjust path if needed
# Create interactive datatable
datatable(
nr_data,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
),
filter = "top",
rownames = FALSE
)
library(tidyverse)
library(DT)
library(readxl)
library(plotly)
library(readr)
# Load required packages
library(readr)
library(DT)
# Read the CSV file
nr_data <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv")  # If running in RStudio, adjust path if needed
# Create interactive datatable
datatable(
nr_data,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
),
filter = "top",
rownames = FALSE
)
library(tidyverse)
library(DT)
library(readxl)
library(plotly)
library(readr)
library(dplyr)
# Read your Pathway CSV
df <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv")
# Create a new column with clickable PNG links
df <- df %>%
mutate(Link = paste0("<a href='jbrowse/function/pathway/", PathwayID, ".png' target='_blank'>", PathwayID, "</a>"))
# Read your Pathway CSV
df <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv")
# Create a new column with clickable PNG links
df <- df %>%
mutate(Link = paste0("<a href='jbrowse/function/pathway/", PathwayID, ".png' target='_blank'>", PathwayId, "</a>"))
# Read your Pathway CSV
df <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv")
# Create a clickable link column using correct column name
df <- df %>%
mutate(Link = paste0(
"<a href='jbrowse/function/pathway/", PathwayId, ".png' target='_blank'>", PathwayId, "</a>"
))
# Display interactive table with HTML link
datatable(
df,
escape = FALSE,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
)
)
# Read your Pathway CSV
# Read the CSV
df <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/pathway_table.csv")
# Create clickable link column
df <- df %>%
mutate(Link = paste0(
"<a href='jbrowse/function/pathway/", PathwayId, ".png' target='_blank'>", PathwayId, "</a>"
))
# Move Link column to position 3
df <- df %>%
select(1:2, Link, everything())
# Display interactive table
datatable(
df,
escape = FALSE,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
)
)
# Read the GFF3 file (skip comment lines starting with "#")
gff <- read_tsv(
"https://gannet.fish.washington.edu/seashell/bu-github/OCEAN/docs/jbrowse/data/v1/GN.gene.gff3",
comment = "#",
col_names = c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes")
)
# Read the GFF3 file (skip comment lines starting with "#")
gff <- read_tsv(
"../docs/jbrowse/data/v1/GN.gene.gff3",
comment = "#",
col_names = c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes")
)
# Read the GFF3 file (skip comment lines starting with "#")
gff <- read_tsv(
"../docs/jbrowse/data/v1/GN.gene.gff3",
comment = "#",
col_names = c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes")
)
datatable(
gff,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
),
filter = "top"
)
# Read the GFF3 file (skip comment lines starting with "#")
gff <- read_tsv(
"http://gannet.fish.washington.edu/seashell/snaps/gene.gff3",
comment = "#",
col_names = c("seqid", "source", "type", "start", "end", "score", "strand", "phase", "attributes")
)
datatable(
gff,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
),
filter = "top"
)
# Read the CSV file
nr_data <- read_csv("http://gannet.fish.washington.edu/seashell/snaps/nr.csv")
# Subset the relevant columns
nr_subset <- nr_data[, c("query_name", "nr.hit_name", "description", "E value")]
# Create interactive datatable
datatable(
nr_subset,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 4
),
filter = "top",
rownames = FALSE
)
# Read the tab-delimited file from the URL
uniprot_data <- read_tsv("http://gannet.fish.washington.edu/seashell/snaps/uniprot.txt")
# Display as an interactive datatable
datatable(
uniprot_data,
extensions = 'Buttons',
options = list(
dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),
pageLength = 10
),
filter = "top",
rownames = FALSE
)