From 89b4649d01985e946e39f20433a72ea23232541d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 24 Jun 2024 12:52:17 +0100 Subject: [PATCH] Fix docs --- R/accessory.R | 4 ---- man/cond_log2_transform_matrix.Rd | 2 +- man/eselistfromConfig.Rd | 5 ----- man/ggplot_boxplot.Rd | 4 ++-- man/ggplot_densityplot.Rd | 4 ++-- man/plotly_boxplot.Rd | 4 ++-- man/plotly_densityplot.Rd | 4 ++-- man/plotly_quartiles.Rd | 4 ++-- 8 files changed, 11 insertions(+), 20 deletions(-) diff --git a/R/accessory.R b/R/accessory.R index b3ff2c4..1bfaa89 100644 --- a/R/accessory.R +++ b/R/accessory.R @@ -558,10 +558,6 @@ eselistFromYAML <- function(configfile) { #' Build an ExploratorySummarisedExperimentList from a description provided in a list #' #' @param config Hierachical named list with input components. See \code{eselistFromYAML} for detail. -#' @param should_transform A boolean indicating if the log2 transformation should be applied. -#' If TRUE, log2 transformation is applied unconditionally. -#' If FALSE, no transformation is applied. -#' If NULL (default), a conditional transformation based on threshold is applied. #' @param log2_threshold A numeric threshold to determine if the matrix should be log-transformed. #' This is only checked if should_transform is NULL. #' @param log2_assays A string parameter that can be NULL, empty, or a non-empty string. diff --git a/man/cond_log2_transform_matrix.Rd b/man/cond_log2_transform_matrix.Rd index 5ce1557..7929163 100644 --- a/man/cond_log2_transform_matrix.Rd +++ b/man/cond_log2_transform_matrix.Rd @@ -24,7 +24,7 @@ If NULL, a conditional transformation based on threshold is applied.} \item{threshold}{A numeric threshold to determine if the matrix should be log-transformed. This is only checked if should_transform is NULL.} -\item{rmzeros}{A boolean indicating whether to remove zeros from the matrix. +\item{rmzeros}{A boolean indicating whether to remove zeros from the matrix. If TRUE, zeros are removed. Default is FALSE.} \item{small_value}{A small value to add to zero entries before log transformation.} diff --git a/man/eselistfromConfig.Rd b/man/eselistfromConfig.Rd index 94bd146..8ea7acb 100644 --- a/man/eselistfromConfig.Rd +++ b/man/eselistfromConfig.Rd @@ -16,11 +16,6 @@ If non-empty: log2 transformation will be applied unconditionally to specified a \item{log2_threshold}{A numeric threshold to determine if the matrix should be log-transformed. This is only checked if should_transform is NULL.} - -\item{should_transform}{A boolean indicating if the log2 transformation should be applied. -If TRUE, log2 transformation is applied unconditionally. -If FALSE, no transformation is applied. -If NULL (default), a conditional transformation based on threshold is applied.} } \value{ out An ExploratorySummarizedExperimentList object suitable for passing to \code{\link{prepareApp}} diff --git a/man/ggplot_boxplot.Rd b/man/ggplot_boxplot.Rd index c2bf928..9cebb2d 100644 --- a/man/ggplot_boxplot.Rd +++ b/man/ggplot_boxplot.Rd @@ -14,7 +14,7 @@ ggplot_boxplot( base_size = 11, palette_name = "Set1", annotate_samples = FALSE, - should_log = NULL + should_transform = NULL ) } \arguments{ @@ -39,7 +39,7 @@ that function for more info (default: 1.5).} \item{annotate_samples}{Add a suffix to sample labels reflecting their group?} -\item{should_log}{A boolean indicating if the log2 transformation should be applied. +\item{should_transform}{A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.} diff --git a/man/ggplot_densityplot.Rd b/man/ggplot_densityplot.Rd index ac51a1a..c161ea0 100644 --- a/man/ggplot_densityplot.Rd +++ b/man/ggplot_densityplot.Rd @@ -13,7 +13,7 @@ ggplot_densityplot( base_size = 16, palette_name = "Set1", annotate_samples = FALSE, - should_log = NULL + should_transform = NULL ) } \arguments{ @@ -34,7 +34,7 @@ ggplot_densityplot( \item{annotate_samples}{Add a suffix to sample labels reflecting their group?} -\item{should_log}{A boolean indicating if the log2 transformation should be applied. +\item{should_transform}{A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.} diff --git a/man/plotly_boxplot.Rd b/man/plotly_boxplot.Rd index bcb6d14..2a29e18 100644 --- a/man/plotly_boxplot.Rd +++ b/man/plotly_boxplot.Rd @@ -12,7 +12,7 @@ plotly_boxplot( expressiontype = "expression", palette_name = "Set1", annotate_samples = FALSE, - should_log = NULL + should_transform = NULL ) } \arguments{ @@ -31,7 +31,7 @@ plotly_boxplot( \item{annotate_samples}{Add a suffix to sample labels reflecting their group?} -\item{should_log}{A boolean indicating if the log2 transformation should be applied. +\item{should_transform}{A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.} diff --git a/man/plotly_densityplot.Rd b/man/plotly_densityplot.Rd index 4c20161..9207bfe 100644 --- a/man/plotly_densityplot.Rd +++ b/man/plotly_densityplot.Rd @@ -12,7 +12,7 @@ plotly_densityplot( expressiontype = "expression", palette_name = "Set1", annotate_samples = FALSE, - should_log = NULL + should_transform = NULL ) } \arguments{ @@ -31,7 +31,7 @@ plotly_densityplot( \item{annotate_samples}{Add a suffix to sample labels reflecting their group?} -\item{should_log}{A boolean indicating if the log2 transformation should be applied. +\item{should_transform}{A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.} diff --git a/man/plotly_quartiles.Rd b/man/plotly_quartiles.Rd index f10a08b..55c46d8 100644 --- a/man/plotly_quartiles.Rd +++ b/man/plotly_quartiles.Rd @@ -9,7 +9,7 @@ plotly_quartiles( labels = rownames(matrix), expressiontype = "expression", whisker_distance = 1.5, - should_log = NULL + should_transform = NULL ) } \arguments{ @@ -22,7 +22,7 @@ plotly_quartiles( \item{whisker_distance}{IQR multiplier for whiskers, and beyond which to show outliers (see \code{coef} in \code{\link[ggplot2]{geom_boxplot}})} -\item{should_log}{A boolean indicating if the log2 transformation should be applied. +\item{should_transform}{A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.}