From 2122f6dd2871bfe5585fdae720d30f5727ab1755 Mon Sep 17 00:00:00 2001 From: unknown Date: Mon, 19 Feb 2024 20:11:45 +0530 Subject: [PATCH 1/9] updating tm_a_pca document. --- R/tm_a_pca.R | 47 ++++++++++++++++++++++++++-------------------- man/tm_a_pca.Rd | 50 ++++++++++++++++++++++++++++++------------------- 2 files changed, 58 insertions(+), 39 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index c1fda7608..03d52df8e 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -1,20 +1,24 @@ #' Principal component analysis module -#' @md +#' +#' Module conducts principal component analysis (PCA) on a given dataset and offers different +#' ways of visualizing the outcomes, including elbow plot, circle plot, biplot, and eigenvector plot. +#' Additionally, it enables dynamic customization of plot aesthetics, such as opacity, size, and +#' font size, through UI inputs. #' #' @inheritParams teal::module #' @inheritParams shared_params #' @param dat (`data_extract_spec` or `list` of multiple `data_extract_spec`) -#' Columns used to compute PCA. -#' @param alpha optional, (`numeric`) If scalar then the plot points will have a fixed opacity. If a -#' slider should be presented to adjust the plot point opacity dynamically then it can be a vector of -#' length three with `c(value, min, max)`. -#' @param size optional, (`numeric`) If scalar then the plot point sizes will have a fixed size. -#' If a slider should be presented to adjust the plot point sizes dynamically then it can be a -#' vector of length three with `c(value, min, max)`. -#' @param font_size optional, (`numeric`) font size control for title, x-axis label, y-axis label and legend. -#' If scalar then the font size will have a fixed size. If a slider should be presented to adjust the plot -#' point sizes dynamically then it can be a vector of length three with `c(value, min, max)`. -#' +#' specifying columns used to compute PCA. +#' @param alpha (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. +#' - If provided as a scalar, it sets a fixed opacity for plot points. +#' - If provided as a vector, it allows dynamic adjustment of plot point opacity via a slider in the UI. +#' @param size (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. +#' - If provided as a scalar, it sets a fixed size for plot points. +#' - If provided as a vector, it allows dynamic adjustment of plot point sizes via a slider in the UI. +#' @param font_size (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. +#' It controls the font size for plot titles, axis labels, and legends. +#' - If scalar then the font size will have a fixed size. +#' - If provided as a vector, it enables dynamic adjustment of font size via a slider in the UI. #' @templateVar ggnames "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot" #' @template ggplot2_args_multi #' @@ -22,25 +26,28 @@ #' #' @examples #' -#' # ADSL example +# ADSL example +#' library(teal.widgets) #' #' data <- teal_data() #' data <- within(data, { #' library(nestcolor) #' ADSL <- teal.modules.general::rADSL #' }) +#' #' datanames <- c("ADSL") #' datanames(data) <- datanames #' join_keys(data) <- default_cdisc_join_keys[datanames] -#' app <- teal::init( +#' +#' app <- init( #' data = data, -#' modules = teal::modules( -#' teal.modules.general::tm_a_pca( +#' modules = modules( +#' tm_a_pca( #' "PCA", -#' dat = teal.transform::data_extract_spec( +#' dat = data_extract_spec( #' dataname = "ADSL", -#' select = teal.transform::select_spec( -#' choices = teal.transform::variable_choices( +#' select = select_spec( +#' choices = variable_choices( #' data = data[["ADSL"]], c("BMRKR1", "AGE", "EOSDY") #' ), #' selected = c("BMRKR1", "AGE"), @@ -48,7 +55,7 @@ #' ), #' filter = NULL #' ), -#' ggplot2_args = teal.widgets::ggplot2_args( +#' ggplot2_args = ggplot2_args( #' labs = list(subtitle = "Plot generated by PCA Module") #' ) #' ) diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index e01bdbe27..a552b3dff 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -24,7 +24,7 @@ tm_a_pca( For \code{modules()} defaults to \code{"root"}. See \code{Details}.} \item{dat}{(\code{data_extract_spec} or \code{list} of multiple \code{data_extract_spec}) -Columns used to compute PCA.} +specifying columns used to compute PCA.} \item{plot_height}{optional, (\code{numeric}) A vector of length three with \verb{c(value, min and max)} for a slider encoding the plot height.} @@ -45,17 +45,24 @@ For more details see the vignette: \code{vignette("custom-ggplot2-arguments", pa \item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{font_size}{optional, (\code{numeric}) font size control for title, x-axis label, y-axis label and legend. -If scalar then the font size will have a fixed size. If a slider should be presented to adjust the plot -point sizes dynamically then it can be a vector of length three with \code{c(value, min, max)}.} +\item{font_size}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. +It controls the font size for plot titles, axis labels, and legends. +\itemize{ +\item If scalar then the font size will have a fixed size. +\item If provided as a vector, it enables dynamic adjustment of font size via a slider in the UI. +}} -\item{alpha}{optional, (\code{numeric}) If scalar then the plot points will have a fixed opacity. If a -slider should be presented to adjust the plot point opacity dynamically then it can be a vector of -length three with \code{c(value, min, max)}.} +\item{alpha}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. +\itemize{ +\item If provided as a scalar, it sets a fixed opacity for plot points. +\item If provided as a vector, it allows dynamic adjustment of plot point opacity via a slider in the UI. +}} -\item{size}{optional, (\code{numeric}) If scalar then the plot point sizes will have a fixed size. -If a slider should be presented to adjust the plot point sizes dynamically then it can be a -vector of length three with \code{c(value, min, max)}.} +\item{size}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. +\itemize{ +\item If provided as a scalar, it sets a fixed size for plot points. +\item If provided as a vector, it allows dynamic adjustment of plot point sizes via a slider in the UI. +}} \item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} @@ -64,29 +71,34 @@ with text placed before the output to put the output into context. For example a into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } \description{ -Principal component analysis module +Module conducts principal component analysis (PCA) on a given dataset and offers different +ways of visualizing the outcomes, including elbow plot, circle plot, biplot, and eigenvector plot. +Additionally, it enables dynamic customization of plot aesthetics, such as opacity, size, and +font size, through UI inputs. } \examples{ -# ADSL example +library(teal.widgets) data <- teal_data() data <- within(data, { library(nestcolor) ADSL <- teal.modules.general::rADSL }) + datanames <- c("ADSL") datanames(data) <- datanames join_keys(data) <- default_cdisc_join_keys[datanames] -app <- teal::init( + +app <- init( data = data, - modules = teal::modules( - teal.modules.general::tm_a_pca( + modules = modules( + tm_a_pca( "PCA", - dat = teal.transform::data_extract_spec( + dat = data_extract_spec( dataname = "ADSL", - select = teal.transform::select_spec( - choices = teal.transform::variable_choices( + select = select_spec( + choices = variable_choices( data = data[["ADSL"]], c("BMRKR1", "AGE", "EOSDY") ), selected = c("BMRKR1", "AGE"), @@ -94,7 +106,7 @@ app <- teal::init( ), filter = NULL ), - ggplot2_args = teal.widgets::ggplot2_args( + ggplot2_args = ggplot2_args( labs = list(subtitle = "Plot generated by PCA Module") ) ) From 057ae536febdf3ce45c4f7333e080fb3dc844c00 Mon Sep 17 00:00:00 2001 From: unknown Date: Tue, 20 Feb 2024 19:53:24 +0530 Subject: [PATCH 2/9] @m7pr suggestions --- R/tm_a_pca.R | 6 +++--- man/tm_a_pca.Rd | 5 +++-- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index 03d52df8e..4a46b5e78 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -10,8 +10,8 @@ #' @param dat (`data_extract_spec` or `list` of multiple `data_extract_spec`) #' specifying columns used to compute PCA. #' @param alpha (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. -#' - If provided as a scalar, it sets a fixed opacity for plot points. -#' - If provided as a vector, it allows dynamic adjustment of plot point opacity via a slider in the UI. +#' - If provided as a vector of `length==1`, it sets a fixed opacity for plot points. +#' - If provided as a vector of `length>1`, it allows dynamic adjustment of plot point opacity via a slider in the UI. #' @param size (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. #' - If provided as a scalar, it sets a fixed size for plot points. #' - If provided as a vector, it allows dynamic adjustment of plot point sizes via a slider in the UI. @@ -26,7 +26,7 @@ #' #' @examples #' -# ADSL example +#' # ADSL example #' library(teal.widgets) #' #' data <- teal_data() diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index a552b3dff..59645d0a7 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -54,8 +54,8 @@ It controls the font size for plot titles, axis labels, and legends. \item{alpha}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. \itemize{ -\item If provided as a scalar, it sets a fixed opacity for plot points. -\item If provided as a vector, it allows dynamic adjustment of plot point opacity via a slider in the UI. +\item If provided as a vector of \code{length==1}, it sets a fixed opacity for plot points. +\item If provided as a vector of \code{length>1}, it allows dynamic adjustment of plot point opacity via a slider in the UI. }} \item{size}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. @@ -78,6 +78,7 @@ font size, through UI inputs. } \examples{ +# ADSL example library(teal.widgets) data <- teal_data() From eb19d0e488bc089c2451470843f9b192229aeaaf Mon Sep 17 00:00:00 2001 From: unknown Date: Tue, 20 Feb 2024 20:12:31 +0530 Subject: [PATCH 3/9] adding return statment --- R/tm_a_pca.R | 10 ++++++++-- man/tm_a_pca.Rd | 4 ++++ 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index 4a46b5e78..850f2f1a4 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -22,7 +22,7 @@ #' @templateVar ggnames "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot" #' @template ggplot2_args_multi #' -#' @export +#' @return Object of class `teal_module` to be used in `teal` applications. #' #' @examples #' @@ -64,6 +64,9 @@ #' if (interactive()) { #' shinyApp(app$ui, app$server) #' } +#' +#' @export +#' tm_a_pca <- function(label = "Principal Component Analysis", dat, plot_height = c(600, 200, 2000), @@ -139,7 +142,8 @@ tm_a_pca <- function(label = "Principal Component Analysis", ) } - +# UI function for the PCA module +# This function defines the UI elements for the PCA analysis, including plot settings and data selection. ui_a_pca <- function(id, ...) { ns <- NS(id) args <- list(...) @@ -250,6 +254,8 @@ ui_a_pca <- function(id, ...) { ) } +# Server function for the PCA module +# This function handles the server-side logic for PCA analysis, including data processing and plot generation. srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, plot_width, ggplot2_args) { with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI") diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index 59645d0a7..305c79c66 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -70,6 +70,9 @@ with text placed before the output to put the output into context. For example a \item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} } +\value{ +Object of class \code{teal_module} to be used in \code{teal} applications. +} \description{ Module conducts principal component analysis (PCA) on a given dataset and offers different ways of visualizing the outcomes, including elbow plot, circle plot, biplot, and eigenvector plot. @@ -116,4 +119,5 @@ app <- init( if (interactive()) { shinyApp(app$ui, app$server) } + } From 7cfd76587c3250c1b851be783d508467064033d3 Mon Sep 17 00:00:00 2001 From: unknown Date: Thu, 22 Feb 2024 18:15:05 +0530 Subject: [PATCH 4/9] updating font_size description --- R/tm_a_pca.R | 4 ++-- man/tm_a_pca.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index bceaccd46..eae3d02fc 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -17,8 +17,8 @@ #' - If provided as a vector, it allows dynamic adjustment of plot point sizes via a slider in the UI. #' @param font_size (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. #' It controls the font size for plot titles, axis labels, and legends. -#' - If scalar then the font size will have a fixed size. -#' - If provided as a vector, it enables dynamic adjustment of font size via a slider in the UI. +#' - If vector of `length==1` then the font size will have a fixed size. +#' - If vector of `length>1`, it enables dynamic adjustment of font size via a slider in the UI. #' @templateVar ggnames "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot" #' @template ggplot2_args_multi #' diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index 8618545b9..a93f6d146 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -48,8 +48,8 @@ rotate by default (\code{FALSE}).} \item{font_size}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. It controls the font size for plot titles, axis labels, and legends. \itemize{ -\item If scalar then the font size will have a fixed size. -\item If provided as a vector, it enables dynamic adjustment of font size via a slider in the UI. +\item If vector of \code{length==1} then the font size will have a fixed size. +\item If vector of \code{length>1}, it enables dynamic adjustment of font size via a slider in the UI. }} \item{alpha}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. From 6f8ecd1b941ce7c2c38f788e48ec5cfed026fdfc Mon Sep 17 00:00:00 2001 From: kartikeya kirar Date: Thu, 22 Feb 2024 20:02:58 +0530 Subject: [PATCH 5/9] Update R/tm_a_pca.R Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> Signed-off-by: kartikeya kirar --- R/tm_a_pca.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index eae3d02fc..d21f15333 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -25,7 +25,7 @@ #' @examples #' library(teal.widgets) #' -#' # General data example +#' # general data example #' data <- teal_data() #' data <- within(data, { #' library(nestcolor) From 6b9f854e56ca4152cea5d30b4bb0a199a0644bfb Mon Sep 17 00:00:00 2001 From: unknown Date: Fri, 23 Feb 2024 14:33:29 +0530 Subject: [PATCH 6/9] updating docuement --- R/tm_a_pca.R | 28 ++++++++++++++-------------- man/tm_a_pca.Rd | 22 ++++++++++------------ 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index eae3d02fc..283b04ea8 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -9,23 +9,23 @@ #' @inheritParams shared_params #' @param dat (`data_extract_spec` or `list` of multiple `data_extract_spec`) #' specifying columns used to compute PCA. -#' @param alpha (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. -#' - If provided as a vector of `length==1`, it sets a fixed opacity for plot points. -#' - If provided as a vector of `length>1`, it allows dynamic adjustment of plot point opacity via a slider in the UI. -#' @param size (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. -#' - If provided as a scalar, it sets a fixed size for plot points. -#' - If provided as a vector, it allows dynamic adjustment of plot point sizes via a slider in the UI. -#' @param font_size (`numeric`, optional) value or a vector of length three in the form `c(value, min, max)`. +#' @param alpha (`numeric`, optional) Specifies point opacity. +#' - If vector of `length==1` then the plot points will have a fixed opacity. +#' - while vector of `value`, `min`, and `max` allows dynamic adjustment. +#' @param size (`numeric`, optional) Specifies point size. +#' - If vector of `length==1` then the plot point sizes will have a fixed size +#' - while vector of `value`, `min`, and `max` allows dynamic adjustment. +#' @param font_size (`numeric`, optional) Specifies font size. #' It controls the font size for plot titles, axis labels, and legends. -#' - If vector of `length==1` then the font size will have a fixed size. -#' - If vector of `length>1`, it enables dynamic adjustment of font size via a slider in the UI. +#' - If vector of `length==1` then the font sizes will have a fixed size. +#' - while vector of `value`, `min`, and `max` allows dynamic adjustment. #' @templateVar ggnames "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot" #' @template ggplot2_args_multi #' #' @examples #' library(teal.widgets) #' -#' # General data example +#' # general data example #' data <- teal_data() #' data <- within(data, { #' library(nestcolor) @@ -56,7 +56,6 @@ #' ) #' ) #' ) -#' #' if (interactive()) { #' shinyApp(app$ui, app$server) #' } @@ -92,7 +91,6 @@ #' ) #' ) #' ) -#' #' if (interactive()) { #' shinyApp(app$ui, app$server) #' } @@ -175,7 +173,8 @@ tm_a_pca <- function(label = "Principal Component Analysis", } # UI function for the PCA module -# This function defines the UI elements for the PCA analysis, including plot settings and data selection. +#' @noRd +#' @keywords internal ui_a_pca <- function(id, ...) { ns <- NS(id) args <- list(...) @@ -287,7 +286,8 @@ ui_a_pca <- function(id, ...) { } # Server function for the PCA module -# This function handles the server-side logic for PCA analysis, including data processing and plot generation. +#' @noRd +#' @keywords internal srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, plot_width, ggplot2_args) { with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI") diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index a93f6d146..a664ab2d4 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -45,23 +45,23 @@ For more details see the vignette: \code{vignette("custom-ggplot2-arguments", pa \item{rotate_xaxis_labels}{optional, (\code{logical}) Whether to rotate plot X axis labels. Does not rotate by default (\code{FALSE}).} -\item{font_size}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. +\item{font_size}{(\code{numeric}, optional) Specifies font size. It controls the font size for plot titles, axis labels, and legends. \itemize{ -\item If vector of \code{length==1} then the font size will have a fixed size. -\item If vector of \code{length>1}, it enables dynamic adjustment of font size via a slider in the UI. +\item If vector of \code{length==1} then the font sizes will have a fixed size. +\item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} -\item{alpha}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. +\item{alpha}{(\code{numeric}, optional) Specifies point opacity. \itemize{ -\item If provided as a vector of \code{length==1}, it sets a fixed opacity for plot points. -\item If provided as a vector of \code{length>1}, it allows dynamic adjustment of plot point opacity via a slider in the UI. +\item If vector of \code{length==1} then the plot points will have a fixed opacity. +\item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} -\item{size}{(\code{numeric}, optional) value or a vector of length three in the form \code{c(value, min, max)}. +\item{size}{(\code{numeric}, optional) Specifies point size. \itemize{ -\item If provided as a scalar, it sets a fixed size for plot points. -\item If provided as a vector, it allows dynamic adjustment of plot point sizes via a slider in the UI. +\item If vector of \code{length==1} then the plot point sizes will have a fixed size +\item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} \item{pre_output}{(\code{shiny.tag}, optional)\cr @@ -79,7 +79,7 @@ font size, through UI inputs. \examples{ library(teal.widgets) -# General data example +# general data example data <- teal_data() data <- within(data, { library(nestcolor) @@ -110,7 +110,6 @@ app <- init( ) ) ) - if (interactive()) { shinyApp(app$ui, app$server) } @@ -146,7 +145,6 @@ app <- init( ) ) ) - if (interactive()) { shinyApp(app$ui, app$server) } From 63a8163938ebc9faff1cff1ece941e2d07f152d8 Mon Sep 17 00:00:00 2001 From: unknown Date: Mon, 26 Feb 2024 18:35:11 +0530 Subject: [PATCH 7/9] removing internal tag --- R/tm_a_pca.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index 283b04ea8..f129d482a 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -174,7 +174,6 @@ tm_a_pca <- function(label = "Principal Component Analysis", # UI function for the PCA module #' @noRd -#' @keywords internal ui_a_pca <- function(id, ...) { ns <- NS(id) args <- list(...) @@ -287,7 +286,6 @@ ui_a_pca <- function(id, ...) { # Server function for the PCA module #' @noRd -#' @keywords internal srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, plot_width, ggplot2_args) { with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI") From ad858bc354c046b62ebaf34ab59ec0c17efd5c65 Mon Sep 17 00:00:00 2001 From: unknown Date: Mon, 26 Feb 2024 18:40:18 +0530 Subject: [PATCH 8/9] removed the @noRd tag --- R/tm_a_pca.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index f129d482a..1128e9c02 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -173,7 +173,6 @@ tm_a_pca <- function(label = "Principal Component Analysis", } # UI function for the PCA module -#' @noRd ui_a_pca <- function(id, ...) { ns <- NS(id) args <- list(...) @@ -285,7 +284,6 @@ ui_a_pca <- function(id, ...) { } # Server function for the PCA module -#' @noRd srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, plot_width, ggplot2_args) { with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI") From c8a2d4293c93c0792aeca267f1e3b27a70e57ac9 Mon Sep 17 00:00:00 2001 From: unknown Date: Mon, 26 Feb 2024 18:42:14 +0530 Subject: [PATCH 9/9] adding space around == --- R/tm_a_pca.R | 6 +++--- man/tm_a_pca.Rd | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R index 1128e9c02..43cbb3fba 100644 --- a/R/tm_a_pca.R +++ b/R/tm_a_pca.R @@ -10,14 +10,14 @@ #' @param dat (`data_extract_spec` or `list` of multiple `data_extract_spec`) #' specifying columns used to compute PCA. #' @param alpha (`numeric`, optional) Specifies point opacity. -#' - If vector of `length==1` then the plot points will have a fixed opacity. +#' - If vector of `length == 1` then the plot points will have a fixed opacity. #' - while vector of `value`, `min`, and `max` allows dynamic adjustment. #' @param size (`numeric`, optional) Specifies point size. -#' - If vector of `length==1` then the plot point sizes will have a fixed size +#' - If vector of `length == 1` then the plot point sizes will have a fixed size #' - while vector of `value`, `min`, and `max` allows dynamic adjustment. #' @param font_size (`numeric`, optional) Specifies font size. #' It controls the font size for plot titles, axis labels, and legends. -#' - If vector of `length==1` then the font sizes will have a fixed size. +#' - If vector of `length == 1` then the font sizes will have a fixed size. #' - while vector of `value`, `min`, and `max` allows dynamic adjustment. #' @templateVar ggnames "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot" #' @template ggplot2_args_multi diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd index a664ab2d4..1ba53f82b 100644 --- a/man/tm_a_pca.Rd +++ b/man/tm_a_pca.Rd @@ -48,19 +48,19 @@ rotate by default (\code{FALSE}).} \item{font_size}{(\code{numeric}, optional) Specifies font size. It controls the font size for plot titles, axis labels, and legends. \itemize{ -\item If vector of \code{length==1} then the font sizes will have a fixed size. +\item If vector of \code{length == 1} then the font sizes will have a fixed size. \item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} \item{alpha}{(\code{numeric}, optional) Specifies point opacity. \itemize{ -\item If vector of \code{length==1} then the plot points will have a fixed opacity. +\item If vector of \code{length == 1} then the plot points will have a fixed opacity. \item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }} \item{size}{(\code{numeric}, optional) Specifies point size. \itemize{ -\item If vector of \code{length==1} then the plot point sizes will have a fixed size +\item If vector of \code{length == 1} then the plot point sizes will have a fixed size \item while vector of \code{value}, \code{min}, and \code{max} allows dynamic adjustment. }}