Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE----------------
## For links
library("BiocStyle")
## Track time spent on making the vignette
startTime <- Sys.time()
## Bib setup
library("RefManageR")
## Write bibliography information
bib <- c(
R = citation(),
BiocStyle = citation("BiocStyle")[1],
knitr =bibentry(
bibtype = "InCollection",
booktitle = "Implementing Reproducible Computational Research",
title = "knitr: A Comprehensive Tool for Reproducible Research in R",
author = as.person("Yihui Xie [aut]"),
editor = as.person("Victoria Stodden, Friedrich Leisch, Roger D. Peng"),
year = "2014",
publisher = "Chapman and Hall/CRC",
isbn = "978-1466561595",
url = "https://www.routledge.com/Implementing-Reproducible-Research/Stodden-Leisch-Peng/p/book/9781466561595"
),
Matrix = citation("Matrix")[1],
RefManageR = citation("RefManageR")[1],
rmarkdown = citation("rmarkdown")[1],
S4Vectors = citation("S4Vectors")[1],
sessioninfo = citation("sessioninfo")[1]
)
## ----'install', eval = FALSE--------------------------------------------------
# install.packages("SRTsim")
## ----setup, message = FALSE, warning = FALSE----------------------------------
library("SRTsim")
## ----'reference-based tissue-wise simulation'---------------------------------
## explore example SRT data
str(exampleLIBD)
example_count <- exampleLIBD$count
example_loc <- exampleLIBD$info[,c("imagecol","imagerow","layer")]
colnames(example_loc) <- c("x","y","label")
## create a SRT object
simSRT <- createSRT(count_in=example_count,loc_in =example_loc)
## Set a seed for reproducible simulation
set.seed(1)
## Estimate model parameters for data generation
simSRT1 <- srtsim_fit(simSRT,sim_schem="tissue")
## Generate synthetic data with estimated parameters
simSRT1 <- srtsim_count(simSRT1)
## Explore the synthetic data
simCounts(simSRT1)[1:5,1:5]
simcolData(simSRT1)
## ----'reference-based domain-specific simulation'-----------------------------
## Set a seed for reproducible simulation
set.seed(1)
## Estimate model parameters for data generation
simSRT2 <- srtsim_fit(simSRT,sim_scheme='domain')
## Generate synthetic data with estimated parameters
simSRT2 <- srtsim_count(simSRT2)
## Explore the synthetic data
simCounts(simSRT2)[1:5,1:5]
## ----'tissue simulation metrics comparison'-----------------------------------
## Compute metrics
simSRT1 <- compareSRT(simSRT1)
## Visualize Metrics
visualize_metrics(simSRT1)
## ----'pattern comparison'-----------------------------------------------------
visualize_gene(simsrt=simSRT1,plotgn = "ENSG00000183036",rev_y=TRUE)
visualize_gene(simsrt=simSRT2,plotgn = "ENSG00000168314",rev_y=TRUE)
## ----createVignette, eval=FALSE-----------------------------------------------
# ## Create the vignette
# library("rmarkdown")
# system.time(render("SRTsim.Rmd"))
#
# ## Extract the R code
# library("knitr")
# knit("SRTsim.Rmd", tangle = TRUE)
## ----reproduce1, echo=FALSE---------------------------------------------------
## Date the vignette was generated
Sys.time()
## ----reproduce2, echo=FALSE---------------------------------------------------
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)
## ----reproduce3, echo=FALSE---------------------------------------------------
## Session info
library("sessioninfo")
original <- options("width")
options(width = 120)
session_info()
options(original)
## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE, message = FALSE----
## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))
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