dtOptions <- list(
orderClasses = TRUE,
pageLength = 10,
order = list(0, "desc"),
scrollX = TRUE,
deferRender = TRUE,
scrollCollapse = TRUE
)
#' Generate list of default options
#'
#' When runninng the shiny app, create the global variable
#' \code{defaultInput <- defaultInput()}. When running
#' functions from ShinyLipids outside of the Shiny app,
#' generate the input list normally created by the web interface
#' with \code{input <- defaultInput()}.
#'
#' @return :: list. A list of default options to be assigned to \code{input}
#' @export
defaultInput <- function() {
list(
aesX = "class",
aesColor = "sample",
aesFacetCol = "",
aesFacetRow = "",
# Filtering
categoryToSelect = NULL,
lipidClassToSelect = NULL,
functionalCategoryToSelect = NULL,
filterLengthRange = c(0L, 100L),
filterDoubleBondsRange = c(0L, 100L),
filterOhRange = c(0L, 100L),
samplesToSelect = NULL,
samplesToRemove = NULL,
replicatesToSelect = NULL,
replicatesToRemove = NULL,
technicalReplicatesToRemove = NULL,
imputeMissingAs0 = TRUE,
# Standardization
summariseTechnicalReplicates = TRUE,
baselineSample = "",
standardizationFeatures = c(""),
standardizeWithinTechnicalReplicate = TRUE,
# Sample selection
samplesToSelect = NULL,
samplesToRemove = NULL,
replicatesToSelect = NULL,
replicatesToRemove = NULL,
# Plotting, main plot
errorbarType = "None",
mainPlotAdditionalOptions = list("points", "bars"),
mainWidth = 20,
mainHeight = 10,
pcaWidth = 10,
pcaHeight = 10,
# heatmap
heatWidth = 20,
heatHeight = 10,
heatColor = "viridis",
heatLogScale = FALSE,
heatLabSize = 9,
# Dimensionality reduction
pcaCrossValidationMethod = "none",
pcaNumberPrincipalComponents = 4,
pcaCenter = TRUE,
pcaScale = TRUE,
pcaLabels = FALSE,
drawPcaConvexHull = TRUE,
pcaPointSize = 5,
pcaVectors = TRUE
)
}
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