## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE----------------
## For links
library("BiocStyle")
## Track time spent on making the vignette
#startTime <- Sys.time()
## Bib setup
library("RefManageR")
## Write bibliography information
bib <- c(
R = citation(),
BiocStyle = citation("BiocStyle")[1],
DT = citation("DT")[1],
ggplot2 = citation("ggplot2")[1],
golem = citation("golem")[1],
knitr = citation("knitr")[3],
plotly = citation("plotly")[1],
RColorBrewer = citation("RColorBrewer")[1],
RefManageR = citation("RefManageR")[1],
rmarkdown = citation("rmarkdown")[1],
shiny = citation("shiny")[1],
testthat = citation("testthat")[1],
biocthis = citation("biocthis")[1],
shinyjs = citation("shinyjs")[1],
shinyFiles = citation("shinyFiles")[1],
plyr = citation("plyr")[1],
data.table = citation("data.table")[1],
stringr = citation("stringr")[1],
stringdist = citation("stringdist")[1],
plot3D = citation("plot3D")[1],
gridExtra = citation("gridExtra")[1],
dplyr = citation("dplyr")[1],
pryr = citation("pryr")[1],
shinyBS = citation("shinyBS")[1],
fs = citation("fs")[1]
)
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
error = FALSE,
warning = FALSE,
message = FALSE,
crop = NULL
)
## ----echo=FALSE, out.width='50%', fig.align='center'--------------------------
knitr::include_graphics(path = system.file("app", "www", "tripr.png",
package="tripr", mustWork=TRUE))
## ----eval = FALSE-------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE)) {
# install.packages("BiocManager")
# }
#
# BiocManager::install("tripr")
#
# ## Check that you have a valid Bioconductor installation
# BiocManager::valid()
## ----setup--------------------------------------------------------------------
library(tripr)
## ----demostart, eval=FALSE----------------------------------------------------
# tripr::run_app()
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www", "upload_data.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www", "Preselection.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"Preselection_Clean_table.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www", "Selection.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www", "Selection_visual.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"pipeline_overview.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"Clonotypes_pipeline.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"clonotypes_tab.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"highly_similar_pipeline.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"highly_sim_clono_tab.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"repertoires_pipeline.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"repertoires_tab.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"mv_pipeline.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"multiple_tab.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"insert_identity_pipeline.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"Alignment_pipeline.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"alignment_tab.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"visual_clono.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"hist3d_visual.png",
package="tripr", mustWork=TRUE))
## ----echo=FALSE, out.width='100%', fig.align='center'-------------------------
knitr::include_graphics(path = system.file("app", "www",
"overview.png",
package="tripr", mustWork=TRUE))
## ----eval = FALSE-------------------------------------------------------------
# ?tripr::run_TRIP
## ----eval=FALSE---------------------------------------------------------------
# fs::path_package("extdata", "dataset", package = "tripr")
## ----eval=FALSE---------------------------------------------------------------
# c("1_Summary.txt", "2_IMGT-gapped-nt-sequences.txt",
# "4_IMGT-gapped-AA-sequences.txt", "6_Junction.txt")
## ----eval=FALSE---------------------------------------------------------------
# datapath <- fs::path_package("extdata", "dataset", package="tripr")
# output_path <- tools::R_user_dir("tripr", which="cache")
# cell <- "Bcell"
# preselection <- "1,2,3,4C:W"
# selection <- "5"
# filelist <- c("1_Summary.txt",
# "2_IMGT-gapped-nt-sequences.txt",
# "4_IMGT-gapped-AA-sequences.txt",
# "6_Junction.txt")
# throughput <- "High Throughput"
# preselection <- "1,2,3,4C:W"
# selection <- "5"
# identity_range <- "88:100"
# pipeline <- "1"
# select_clonotype <- "V Gene + CDR3 Amino Acids"
#
# run_TRIP(
# datapath=datapath,
# output_path=output_path,
# filelist=filelist,
# cell=cell,
# throughput=throughput,
# preselection=preselection,
# selection=selection,
# identity_range=identity_range,
# pipeline=pipeline,
# select_clonotype=select_clonotype)
## ----'citation'---------------------------------------------------------------
## Citation info
citation("tripr")
## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()
## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE, message = FALSE----
## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))