Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
eval = TRUE,
collapse = TRUE,
# results = "asis",
include = TRUE,
echo = TRUE,
warning = TRUE,
message = TRUE,
error = TRUE,
# tidy = FALSE,
# crop = TRUE,
# autodep = TRUE,
fig.align = "center",
fig.pos = "!h",
cache = FALSE
)
## ----logo, echo = FALSE, out.width = "150px"----------------------------------
knitr::include_graphics(path = "nacho_hex.png")
## ---- eval = FALSE------------------------------------------------------------
# # Install NACHO from CRAN:
# install.packages("NACHO")
#
# # Or the the development version from GitHub:
# # install.packages("remotes")
# remotes::install_github("mcanouil/NACHO")
## ---- message = FALSE---------------------------------------------------------
# Load NACHO
library(NACHO)
## ---- echo = FALSE, results = "asis"------------------------------------------
cat(readLines(system.file("app", "www", "about-nacho.md", package = "NACHO"))[-c(1, 2)], sep = "\n")
## ---- echo = FALSE, results = "asis"------------------------------------------
print(citation("NACHO"), "html")
## ---- echo = FALSE, comment = ""----------------------------------------------
print(citation("NACHO"), "bibtex")
## ----ex1, eval = FALSE--------------------------------------------------------
# library(NACHO)
# data(GSE74821)
# visualise(GSE74821)
## ----ex1-fig, echo = FALSE, out.width = "650px"-------------------------------
knitr::include_graphics(path = "README-visualise.png")
## ----geo-down, echo = FALSE, warning = FALSE, message = FALSE, error = FALSE----
gse <- try(GEOquery::getGEO("GSE70970"), silent = TRUE)
if (inherits(gse, "try-error")) { # when GEOquery is down
cons <- showConnections(all = TRUE)
icons <- which(grepl("GSE70970", cons[, "description"])) - 1
for (icon in icons) close(getConnection(icon))
cat(
"Note: `GEOquery` seems to be currently down. Thus, the following code was not executed.\n"
)
}
## ----ex2, results = "hide", message = FALSE, warning = FALSE, eval = !inherits(gse, "try-error")----
library(GEOquery)
# Download data
gse <- getGEO("GSE70970")
getGEOSuppFiles(GEO = "GSE70970", baseDir = tempdir())
# Unzip data
untar(
tarfile = file.path(tempdir(), "GSE70970", "GSE70970_RAW.tar"),
exdir = file.path(tempdir(), "GSE70970", "Data")
)
# Get phenotypes and add IDs
targets <- pData(phenoData(gse[[1]]))
targets$IDFILE <- list.files(file.path(tempdir(), "GSE70970", "Data"))
## ---- echo = FALSE, message = FALSE, warning = FALSE, eval = !inherits(gse, "try-error")----
targets[1:5, unique(c("IDFILE", names(targets)))]
## ----ex3, eval = !inherits(gse, "try-error")----------------------------------
GSE70970_sum <- load_rcc(
data_directory = file.path(tempdir(), "GSE70970", "Data"), # Where the data is
ssheet_csv = targets, # The samplesheet
id_colname = "IDFILE", # Name of the column that contains the unique identfiers
housekeeping_genes = NULL, # Custom list of housekeeping genes
housekeeping_predict = TRUE, # Whether or not to predict the housekeeping genes
normalisation_method = "GEO", # Geometric mean or GLM
n_comp = 5 # Number indicating how many principal components should be computed.
)
## ---- echo = FALSE, results = "hide", eval = !inherits(gse, "try-error")------
unlink(file.path(tempdir(), "GSE70970"), recursive = TRUE)
## -----------------------------------------------------------------------------
# visualise(GSE70970_sum)
## ----ex5, eval = !inherits(gse, "try-error")----------------------------------
print(GSE70970_sum[["housekeeping_genes"]])
## ----intext, eval = !inherits(gse, "try-error"), echo = FALSE, results = "asis"----
cat(
"Let's say _", GSE70970_sum[["housekeeping_genes"]][1],
"_ and _", GSE70970_sum[["housekeeping_genes"]][2],
"_ are not suitable, therefore, you want to exclude these genes from the normalisation process.",
sep = ""
)
## ---- eval = !inherits(gse, "try-error")--------------------------------------
my_housekeeping <- GSE70970_sum[["housekeeping_genes"]][-c(1, 2)]
print(my_housekeeping)
## ----ex7, eval = !inherits(gse, "try-error")----------------------------------
GSE70970_norm <- normalise(
nacho_object = GSE70970_sum,
housekeeping_genes = my_housekeeping,
housekeeping_predict = FALSE,
housekeeping_norm = TRUE,
normalisation_method = "GEO",
remove_outliers = TRUE
)
## ---- eval = FALSE------------------------------------------------------------
# autoplot(
# object = GSE74821,
# x = "BD",
# colour = "CartridgeID",
# size = 0.5,
# show_legend = TRUE
# )
## ---- echo = FALSE, results = "asis"------------------------------------------
metrics <- c(
"BD" = "Binding Density",
"FoV" = "Imaging",
"PCL" = "Positive Control Linearity",
"LoD" = "Limit of Detection",
"Positive" = "Positive Controls",
"Negative" = "Negative Controls",
"Housekeeping" = "Housekeeping Genes",
"PN" = "Positive Controls vs. Negative Controls",
"ACBD" = "Average Counts vs. Binding Density",
"ACMC" = "Average Counts vs. Median Counts",
"PCA12" = "Principal Component 1 vs. 2",
"PCAi" = "Principal Component scree plot",
"PCA" = "Principal Components planes",
"PFNF" = "Positive Factor vs. Negative Factor",
"HF" = "Housekeeping Factor",
"NORM" = "Normalisation Factor"
)
for (imetric in seq_along(metrics)) {
cat("\n\n###", metrics[imetric], "\n\n")
print(autoplot(object = GSE74821, x = names(metrics[imetric])))
cat("\n")
}
## ----deploy, eval = FALSE-----------------------------------------------------
# deploy(directory = "/srv/shiny-server", app_name = "NACHO")
## ----app, eval = FALSE--------------------------------------------------------
# shiny::runApp(system.file("app", package = "NACHO"))
## ----app-fig, echo = FALSE, out.width = "650px"-------------------------------
knitr::include_graphics(path = "README-app.png")
## ---- eval = FALSE------------------------------------------------------------
# render(
# nacho_object = GSE74821,
# colour = "CartridgeID",
# output_file = "NACHO_QC.html",
# output_dir = ".",
# size = 0.5,
# show_legend = TRUE,
# clean = TRUE
# )
## ----print, results = "asis"--------------------------------------------------
print(
x = GSE74821,
colour = "CartridgeID",
size = 0.5,
show_legend = TRUE,
echo = TRUE,
title_level = 3
)
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