From a59315d089f0542afef281821fca24161a5931dd Mon Sep 17 00:00:00 2001
From: Witold Wolski <wewolski@gmail.com>
Date: Mon, 22 Jan 2024 21:13:12 +0100
Subject: [PATCH] fix doc

---
 R/tidyMS_aggregation.R      | 19 ++++++++-----------
 R/tidyMS_missigness.R       |  6 +++---
 man/missigness_histogram.Rd |  6 +++---
 man/plot_estimate.Rd        | 19 ++++++++-----------
 4 files changed, 22 insertions(+), 28 deletions(-)

diff --git a/R/tidyMS_aggregation.R b/R/tidyMS_aggregation.R
index a08bb40d9..ee135ad0f 100644
--- a/R/tidyMS_aggregation.R
+++ b/R/tidyMS_aggregation.R
@@ -637,23 +637,20 @@ estimate_intensity <- function(data, config, .func)
 #' @export
 #' @examples
 #'
-#' dd <- prolfqua_data('data_ionstar')$filtered()
-#'
-#' config <- old2new(dd$config)
-#' data <- dd$data
+#' istar <- sim_lfq_data_peptide_config()
+#' config <- istar$config
+#' analysis <- istar$data
 #'
-#' data <- prolfqua::transform_work_intensity(data, config, log2)
-#' bbMed <- estimate_intensity(data, config, .func = medpolish_estimate_dfconfig)
-#' tmpMed <- plot_estimate(data, config, bbMed$data, bbMed$config)
+#' analysis <- prolfqua::transform_work_intensity(analysis, config, log2)
+#' bbMed <- estimate_intensity(analysis, config, .func = medpolish_estimate_dfconfig)
+#' tmpMed <- plot_estimate(analysis, config, bbMed$data, bbMed$config)
 #' stopifnot("ggplot" %in% class(tmpMed$plots[[1]]))
 #' stopifnot("ggplot" %in% class(tmpMed$plots[[2]]))
-#' tmpMed$plots[[3]]
 #'
-#' bbRob <- estimate_intensity(data, config, .func = rlm_estimate_dfconfig)
-#' tmpRob <- plot_estimate(data, config, bbRob$data, bbRob$config)
+#' bbRob <- estimate_intensity(analysis, config, .func = rlm_estimate_dfconfig)
+#' tmpRob <- plot_estimate(analysis, config, bbRob$data, bbRob$config)
 #' stopifnot("ggplot" %in% class(tmpRob$plots[[1]]))
 #' stopifnot("ggplot" %in% class(tmpRob$plots[[2]]))
-#' tmpRob$plots[[3]]
 #'
 #'
 plot_estimate <- function(data, config, data_aggr, config_reduced, show.legend= FALSE ){
diff --git a/R/tidyMS_missigness.R b/R/tidyMS_missigness.R
index 76aa9e4dc..820256b65 100644
--- a/R/tidyMS_missigness.R
+++ b/R/tidyMS_missigness.R
@@ -474,12 +474,12 @@ get_imputed_contrasts <- function(pepIntensity,
 #' istar <- sim_lfq_data_peptide_config()
 #' config <- istar$config
 #' analysis <- istar$data
-#' xx <- complete_cases(data, config)
+#' xx <- complete_cases(analysis, config)
 #' pl <- missigness_histogram(xx, config)
 #'
-#' pl <- missigness_histogram(data, config, showempty=FALSE)
+#' pl <- missigness_histogram(analysis, config, showempty=FALSE)
 #' stopifnot("ggplot" %in% class(pl))
-#' pl <- missigness_histogram(data, config, showempty=TRUE)
+#' pl <- missigness_histogram(analysis, config, showempty=TRUE)
 #' stopifnot("ggplot" %in% class(pl))
 #'
 missigness_histogram <- function(x,
diff --git a/man/missigness_histogram.Rd b/man/missigness_histogram.Rd
index 790d6f051..e2595d09a 100644
--- a/man/missigness_histogram.Rd
+++ b/man/missigness_histogram.Rd
@@ -20,12 +20,12 @@ Histogram summarizing missigness
 istar <- sim_lfq_data_peptide_config()
 config <- istar$config
 analysis <- istar$data
-xx <- complete_cases(data, config)
+xx <- complete_cases(analysis, config)
 pl <- missigness_histogram(xx, config)
 
-pl <- missigness_histogram(data, config, showempty=FALSE)
+pl <- missigness_histogram(analysis, config, showempty=FALSE)
 stopifnot("ggplot" \%in\% class(pl))
-pl <- missigness_histogram(data, config, showempty=TRUE)
+pl <- missigness_histogram(analysis, config, showempty=TRUE)
 stopifnot("ggplot" \%in\% class(pl))
 
 }
diff --git a/man/plot_estimate.Rd b/man/plot_estimate.Rd
index 5f8fb4153..08c89b9e4 100644
--- a/man/plot_estimate.Rd
+++ b/man/plot_estimate.Rd
@@ -20,23 +20,20 @@ Plot feature data and result of aggregation
 }
 \examples{
 
-dd <- prolfqua_data('data_ionstar')$filtered()
+istar <- sim_lfq_data_peptide_config()
+config <- istar$config
+analysis <- istar$data
 
-config <- old2new(dd$config)
-data <- dd$data
-
-data <- prolfqua::transform_work_intensity(data, config, log2)
-bbMed <- estimate_intensity(data, config, .func = medpolish_estimate_dfconfig)
-tmpMed <- plot_estimate(data, config, bbMed$data, bbMed$config)
+analysis <- prolfqua::transform_work_intensity(analysis, config, log2)
+bbMed <- estimate_intensity(analysis, config, .func = medpolish_estimate_dfconfig)
+tmpMed <- plot_estimate(analysis, config, bbMed$data, bbMed$config)
 stopifnot("ggplot" \%in\% class(tmpMed$plots[[1]]))
 stopifnot("ggplot" \%in\% class(tmpMed$plots[[2]]))
-tmpMed$plots[[3]]
 
-bbRob <- estimate_intensity(data, config, .func = rlm_estimate_dfconfig)
-tmpRob <- plot_estimate(data, config, bbRob$data, bbRob$config)
+bbRob <- estimate_intensity(analysis, config, .func = rlm_estimate_dfconfig)
+tmpRob <- plot_estimate(analysis, config, bbRob$data, bbRob$config)
 stopifnot("ggplot" \%in\% class(tmpRob$plots[[1]]))
 stopifnot("ggplot" \%in\% class(tmpRob$plots[[2]]))
-tmpRob$plots[[3]]
 
 
 }