From 912a09f339a9e9ecc84f1d02371150c33dd661e1 Mon Sep 17 00:00:00 2001 From: deeenes Date: Fri, 8 Nov 2024 14:15:14 +0100 Subject: [PATCH] docs rebuild --- NAMESPACE | 84 +++++++++++++++++++++++++++++++++- man/DMA.Rd | 20 ++++++-- man/InspectID.Rd | 18 -------- man/PoolEstimation.Rd | 18 ++++++-- man/PreProcessing.Rd | 20 ++++++-- man/ReplicateSum.Rd | 10 ++++ man/ToyData.Rd | 4 +- man/TranslateID.Rd | 28 ++++++++---- man/VizHeatmap.Rd | 4 +- man/VizPCA.Rd | 4 +- man/VizSuperplot.Rd | 4 +- man/VizVolcano.Rd | 4 +- man/metaproviz_log.Rd | 24 ---------- man/metaproviz_logfile.Rd | 23 ---------- man/metaproviz_set_loglevel.Rd | 23 ---------- 15 files changed, 166 insertions(+), 122 deletions(-) delete mode 100644 man/InspectID.Rd delete mode 100644 man/metaproviz_log.Rd delete mode 100644 man/metaproviz_logfile.Rd delete mode 100644 man/metaproviz_set_loglevel.Rd diff --git a/NAMESPACE b/NAMESPACE index 0323517..5ae45c6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,7 +2,7 @@ export(ClusterORA) export(DMA) -export(InspectID) +export(DetectedID) export(LoadHallmarks) export(LoadKEGG) export(LoadMetalinks) @@ -16,6 +16,7 @@ export(MetaProViz_log) export(MetaProViz_logfile) export(MetaProViz_set_loglevel) export(PoolEstimation) +export(PossibleID) export(PreProcessing) export(ReplicateSum) export(StandardORA) @@ -30,26 +31,87 @@ export(metaproviz_load_config) export(metaproviz_reset_config) export(metaproviz_save_config) importFrom(OmnipathR,config_path) +importFrom(OmnipathR,id_types) importFrom(OmnipathR,load_config) importFrom(OmnipathR,logfile) importFrom(OmnipathR,read_log) importFrom(OmnipathR,reset_config) importFrom(OmnipathR,save_config) importFrom(OmnipathR,set_loglevel) +importFrom(OmnipathR,translate_ids) +importFrom(dplyr,across) +importFrom(dplyr,arrange) +importFrom(dplyr,case_when) importFrom(dplyr,filter) +importFrom(dplyr,first) importFrom(dplyr,group_by) importFrom(dplyr,mutate) +importFrom(dplyr,mutate_all) importFrom(dplyr,n) +importFrom(dplyr,pull) +importFrom(dplyr,relocate) importFrom(dplyr,rename) +importFrom(dplyr,rowwise) importFrom(dplyr,select) +importFrom(dplyr,select_if) +importFrom(dplyr,summarise) +importFrom(dplyr,summarise_all) importFrom(dplyr,summarise_at) +importFrom(dplyr,summarize) +importFrom(dplyr,ungroup) +importFrom(factoextra,fviz_screeplot) importFrom(ggbeeswarm,geom_beeswarm) +importFrom(ggplot2,aes) +importFrom(ggplot2,aes_string) +importFrom(ggplot2,annotate) +importFrom(ggplot2,annotation_custom) +importFrom(ggplot2,autoplot) importFrom(ggplot2,element_rect) +importFrom(ggplot2,geom_abline) +importFrom(ggplot2,geom_bar) +importFrom(ggplot2,geom_boxplot) +importFrom(ggplot2,geom_density) +importFrom(ggplot2,geom_dotplot) +importFrom(ggplot2,geom_histogram) +importFrom(ggplot2,geom_hline) +importFrom(ggplot2,geom_line) +importFrom(ggplot2,geom_point) +importFrom(ggplot2,geom_qq) +importFrom(ggplot2,geom_qq_line) +importFrom(ggplot2,geom_smooth) +importFrom(ggplot2,geom_violin) +importFrom(ggplot2,geom_vline) importFrom(ggplot2,ggplot) importFrom(ggplot2,ggplotGrob) +importFrom(ggplot2,ggplot_build) +importFrom(ggplot2,ggtitle) +importFrom(ggplot2,labs) +importFrom(ggplot2,scale_color_manual) +importFrom(ggplot2,scale_linetype_discrete) +importFrom(ggplot2,scale_x_continuous) +importFrom(ggplot2,scale_y_continuous) +importFrom(ggplot2,stat_summary) importFrom(ggplot2,theme) +importFrom(ggplot2,theme_bw) +importFrom(ggplot2,theme_classic) +importFrom(ggplot2,theme_minimal) +importFrom(ggplot2,xlab) +importFrom(ggplot2,ylab) importFrom(ggpubr,get_legend) +importFrom(ggpubr,stat_pvalue_manual) +importFrom(ggrepel,geom_text_repel) +importFrom(grid,convertUnit) importFrom(grid,unit) +importFrom(gridExtra,grid.arrange) +importFrom(gtools,foldchange2logratio) +importFrom(hash,keys) +importFrom(hash,values) +importFrom(inflection,uik) +importFrom(limma,contrasts.fit) +importFrom(limma,eBayes) +importFrom(limma,lmFit) +importFrom(limma,makeContrasts) +importFrom(limma,topTable) importFrom(logger,log_info) importFrom(logger,log_trace) importFrom(logger,log_warn) @@ -59,22 +121,42 @@ importFrom(magrittr,add) importFrom(magrittr,extract) importFrom(magrittr,extract2) importFrom(magrittr,multiply_by) +importFrom(patchwork,wrap_plots) importFrom(purrr,map) importFrom(purrr,map_chr) importFrom(purrr,map_int) importFrom(purrr,partial) importFrom(purrr,reduce) +importFrom(qcc,mqcc) importFrom(readr,cols) importFrom(readr,read_csv) +importFrom(reshape2,melt) importFrom(rlang,"!!!") importFrom(rlang,"!!") importFrom(rlang,"%||%") importFrom(rlang,":=") +importFrom(rlang,sym) +importFrom(rlang,syms) +importFrom(rstatix,dunn_test) +importFrom(rstatix,games_howell_test) +importFrom(stats,TukeyHSD) +importFrom(stats,aov) +importFrom(stats,bartlett.test) +importFrom(stats,kruskal.test) +importFrom(stats,lm) +importFrom(stats,p.adjust) +importFrom(stats,shapiro.test) importFrom(stringr,str_match) importFrom(stringr,str_sub) +importFrom(stringr,str_to_lower) importFrom(stringr,str_trim) importFrom(tibble,column_to_rownames) importFrom(tibble,rownames_to_column) +importFrom(tidyr,pivot_longer) +importFrom(tidyr,separate) +importFrom(tidyr,unite) +importFrom(tidyselect,everything) +importFrom(tidyselect,starts_with) importFrom(utils,head) importFrom(utils,packageVersion) importFrom(utils,read.csv) diff --git a/man/DMA.Rd b/man/DMA.Rd index fbb67d4..f126fc4 100644 --- a/man/DMA.Rd +++ b/man/DMA.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/DifferentialMetaboliteAnalysis.R \name{DMA} \alias{DMA} -\title{This script allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions.} +\title{This function allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions.} \usage{ DMA( InputData, @@ -27,7 +27,7 @@ DMA( \item{SettingsFile_Sample}{DF which contains metadata information about the samples, which will be combined with your input data based on the unique sample identifiers used as rownames.} -\item{SettingsInfo}{\emph{Optional: } Named vector including the information about the conditions column c(Conditions="ColumnName_SettingsFile"). Can additionally pass information on numerator or denominator c(Numerator = "ColumnName_SettingsFile", Denominator = "ColumnName_SettingsFile") for specifying which comparison(s) will be done (one-vs-one, all-vs-one, all-vs-all). Using =NULL selects all the condition and performs multiple comparison all-vs-all. Log2FC are obtained by dividing the numerator by the denominator, thus positive Log2FC values mean higher expression in the numerator and are presented in the right side on the Volcano plot (For CoRe the Log2Distance). \strong{Default = c(conditions="Conditions", numerator = NULL, denumerator = NULL)}} +\item{SettingsInfo}{\emph{Optional: } Named vector including the information about the conditions column information on numerator or denominator c(Conditions="ColumnName_SettingsFile", Numerator = "ColumnName_SettingsFile", Denominator = "ColumnName_SettingsFile"). Denominator and Numerator will specify which comparison(s) will be done (one-vs-one, all-vs-one, all-vs-all), e.g. Denominator=NULL and Numerator =NULL selects all the condition and performs multiple comparison all-vs-all. Log2FC are obtained by dividing the numerator by the denominator, thus positive Log2FC values mean higher expression in the numerator. \strong{Default = c(conditions="Conditions", numerator = NULL, denumerator = NULL)}} \item{StatPval}{\emph{Optional: } String which contains an abbreviation of the selected test to calculate p.value. For one-vs-one comparisons choose t.test, wilcox.test, "chisq.test", "cor.test" or lmFit (=limma), for one-vs-all or all-vs-all comparison choose aov (=anova), welch(=welch anova), kruskal.test or lmFit (=limma) \strong{Default = "lmFit"}} @@ -43,7 +43,7 @@ DMA( \item{PerformBartlett}{TRUE or FALSE for whether to perform the bartlett.test. \strong{Default = TRUE}} -\item{Transform}{TRUE or FALSE. If TRUE we expect the data to be not log2 transformed and log2 transformation will be performed within the limma function and Log2FC calculation. If FALSE we expect the data to be log2 transformed as this impacts the Log2FC calculation and limma. \strong{default: NULL}} +\item{Transform}{TRUE or FALSE. If TRUE we expect the data to be not log2 transformed and log2 transformation will be performed within the limma function and Log2FC calculation. If FALSE we expect the data to be log2 transformed as this impacts the Log2FC calculation and limma. \strong{Default= TRUE}} \item{SaveAs_Plot}{\emph{Optional: } Select the file type of output plots. Options are svg, png, pdf. \strong{Default = svg}} @@ -51,10 +51,20 @@ DMA( \item{PrintPlot}{\emph{Optional: } TRUE or FALSE, if TRUE Volcano plot is saved as an overview of the results. \strong{Default = TRUE}} -\item{FolderPath}{\emph{Optional:} Path to the folder the results should be saved at. \strong{default: NULL}} +\item{FolderPath}{\emph{Optional:} Path to the folder the results should be saved at. \strong{Default = NULL}} +} +\value{ +Dependent on parameter settings, list of lists will be returned for DMA (DF of each comparison), Shapiro (Includes DF and Plot), Bartlett (Includes DF and Histogram), VST (Includes DF and Plot) and VolcanoPlot (Plots of each comparison). } \description{ -This script allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions. +This function allows you to perform differential metabolite analysis to obtain a Log2FC, pval, padj and tval comparing two or multiple conditions. +} +\examples{ +Intra <- MetaProViz::ToyData("IntraCells_Raw") +Res <- MetaProViz::DMA(InputData=Intra[-c(49:58) ,-c(1:3)], + SettingsFile_Sample=Intra[-c(49:58) , c(1:3)], + SettingsInfo = c(Conditions = "Conditions", Numerator = NULL, Denominator = "HK2")) + } \keyword{Analysis,} \keyword{Differential} diff --git a/man/InspectID.Rd b/man/InspectID.Rd deleted file mode 100644 index 718e883..0000000 --- a/man/InspectID.Rd +++ /dev/null @@ -1,18 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/GetPriorKnoweldge.R -\name{InspectID} -\alias{InspectID} -\title{Inspect ID} -\usage{ -InspectID( - Input_DataFrame, - SettingsInfo = list(OriginalIDcolumn = "MetaboliteID", TranslatedCollapsedIDcolumn = - "chebi_collapsed", Pathway = "term") -) -} -\value{ -Two data frames, the first of which is a summary of the mapping from Original to Translated, and the second of which is the reverse, from Translated to Original, with counts per unique ID and pathway. -} -\description{ -Inspect how well IDs map from the translated format (e.g. PubChem) to the original data format (e.g. KEGG), in terms of direct mapping, or one-to-many relationships. -} diff --git a/man/PoolEstimation.Rd b/man/PoolEstimation.Rd index 3812c81..87a7b76 100644 --- a/man/PoolEstimation.Rd +++ b/man/PoolEstimation.Rd @@ -2,13 +2,13 @@ % Please edit documentation in R/Processing.R \name{PoolEstimation} \alias{PoolEstimation} -\title{Description} +\title{Find metabolites with high variqability across total pool samples} \usage{ PoolEstimation( InputData, SettingsFile_Sample = NULL, SettingsInfo = NULL, - CutoffCV = 100, + CutoffCV = 30, SaveAs_Plot = "svg", SaveAs_Table = "csv", PrintPlot = TRUE, @@ -22,7 +22,7 @@ PoolEstimation( \item{SettingsInfo}{\emph{Optional: } NULL or Named vector including the Conditions and PoolSample information (Name of the Conditions column and Name of the pooled samples in the Conditions in the Input_SettingsFile) : c(Conditions="ColumnNameConditions, PoolSamples=NamePoolCondition. If no Conditions is added in the Input_SettingsInfo, it is assumed that the conditions column is named 'Conditions' in the Input_SettingsFile. ). \strong{Default = NULL}} -\item{CutoffCV}{\emph{Optional: } Filtering cutoff for high variance metabolites using the Coefficient of Variation. \strong{Default = 1}} +\item{CutoffCV}{\emph{Optional: } Filtering cutoff for high variance metabolites using the Coefficient of Variation. \strong{Default = 30}} \item{SaveAs_Plot}{\emph{Optional: } Select the file type of output plots. Options are svg, png, pdf or NULL. \strong{Default = svg}} @@ -32,8 +32,18 @@ PoolEstimation( \item{FolderPath}{\emph{Optional:} Path to the folder the results should be saved at. \strong{default: NULL}} } +\value{ +List with two elements: DF (including input and output table) and Plot (including all plots generated) +} \description{ -Description +Find metabolites with high variqability across total pool samples +} +\examples{ +Intra <- ToyData("IntraCells_Raw") +Res <- PoolEstimation(InputData=Intra[ ,-c(1:3)], + SettingsFile_Sample=Intra[ , c(1:3)], + SettingsInfo = c(PoolSamples = "Pool", Conditions="Conditions")) + } \keyword{Coefficient} \keyword{Variation,} diff --git a/man/PreProcessing.Rd b/man/PreProcessing.Rd index 5b6c850..70b652e 100644 --- a/man/PreProcessing.Rd +++ b/man/PreProcessing.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/Processing.R \name{PreProcessing} \alias{PreProcessing} -\title{Applies 80\%-filtering rule, total-ion count normalization, missing value imputation and HotellingT2 outlier detection} +\title{Modularised Normalization: 80\%-filtering rule, total-ion count normalization, missing value imputation and Outlier Detection: HotellingT2.} \usage{ PreProcessing( InputData, @@ -26,9 +26,9 @@ PreProcessing( \item{SettingsFile_Sample}{DF which contains information about the samples, which will be combined with the input data based on the unique sample identifiers used as rownames.} -\item{SettingsInfo}{NULL or Named vector containing the information about the names of the experimental parameters. c(Conditions="ColumnName_Plot_SettingsFile", Biological_Replicates="ColumnName_Plot_SettingsFile"). Column "Conditions" with information about the sample conditions (e.g. "N" and "T" or "Normal" and "Tumor"), can be used for feature filtering and colour coding in the PCA. Column "BiologicalReplicates" including numerical values. For CoRe = TRUE a CoRe_norm_factor = "Columnname_Input_SettingsFile" and CoRe_media = "Columnname_Input_SettingsFile", have to also be added. Column CoRe_norm_factor is used for normalization and CoRe_media is used to specify the name of the media controls in the Conditions.} +\item{SettingsInfo}{or Named vector containing the information about the names of the experimental parameters. c(Conditions="ColumnName_Plot_SettingsFile", Biological_Replicates="ColumnName_Plot_SettingsFile"). Column "Conditions" with information about the sample conditions (e.g. "N" and "T" or "Normal" and "Tumor"), can be used for feature filtering and colour coding in the PCA. Column "BiologicalReplicates" including numerical values. For CoRe = TRUE a CoRe_norm_factor = "Columnname_Input_SettingsFile" and CoRe_media = "Columnname_Input_SettingsFile", have to also be added. Column CoRe_norm_factor is used for normalization and CoRe_media is used to specify the name of the media controls in the Conditions.} -\item{FeatureFilt}{\emph{Optional: }If NULL, no feature filtering is performed. If set to "Standard" then it applies the 80\%-filtering rule (Bijlsma S. et al., 2006) on the metabolite features on the whole dataset. If is set to "Modified",filtering is done based on the different conditions, thus a column named "Conditions" must be provided in the Input_SettingsFile input file including the individual conditions you want to apply the filtering to (Yang, J et al., 2015). \strong{Default = Modified}} +\item{FeatureFilt}{\emph{Optional: }If NULL, no feature filtering is performed. If set to "Standard" then it applies the 80\%-filtering rule (Bijlsma S. et al., 2006) on the metabolite features on the whole dataset. If is set to "Modified",filtering is done based on the different conditions, thus a column named "Conditions" must be provided in the Input_SettingsFile input file including the individual conditions you want to apply the filtering to (Yang, J et al., 2015). \strong{Default = "Standard"}} \item{FeatureFilt_Value}{\emph{Optional: } Percentage of feature filtering. \strong{Default = 0.8}} @@ -50,8 +50,18 @@ PreProcessing( \item{FolderPath}{\emph{Optional:} Path to the folder the results should be saved at. \strong{default: NULL}} } +\value{ +List with two elements: DF (including all output tables generated) and Plot (including all plots generated) +} \description{ -Applies 80\%-filtering rule, total-ion count normalization, missing value imputation and HotellingT2 outlier detection +Modularised Normalization: 80\%-filtering rule, total-ion count normalization, missing value imputation and Outlier Detection: HotellingT2. +} +\examples{ +Intra <- MetaProViz::ToyData("IntraCells_Raw") +Res <- MetaProViz::PreProcessing(InputData=Intra[-c(49:58) ,-c(1:3)], + SettingsFile_Sample=Intra[-c(49:58) , c(1:3)], + SettingsInfo = c(Conditions = "Conditions", Biological_Replicates = "Biological_Replicates")) + } \keyword{80} \keyword{Count} @@ -62,7 +72,7 @@ Applies 80\%-filtering rule, total-ion count normalization, missing value imputa \keyword{PCA,} \keyword{Total} \keyword{Value} -\keyword{charts,} +\keyword{charts} \keyword{control} \keyword{filtering} \keyword{multivariate} diff --git a/man/ReplicateSum.Rd b/man/ReplicateSum.Rd index be174c5..9be6d87 100644 --- a/man/ReplicateSum.Rd +++ b/man/ReplicateSum.Rd @@ -23,8 +23,18 @@ ReplicateSum( \item{FolderPath}{\emph{Optional:} Path to the folder the results should be saved at. \strong{default: NULL}} } +\value{ +DF with the merged analytical replicates +} \description{ Merges the analytical replicates of an experiment +} +\examples{ +Intra <- ToyData("IntraCells_Raw") +Res <- ReplicateSum(InputData=Intra[-c(49:58) ,-c(1:3)], + SettingsFile_Sample=Intra[-c(49:58) , c(1:3)], + SettingsInfo = c(Conditions="Conditions", Biological_Replicates="Biological_Replicates", Analytical_Replicates="Analytical_Replicates")) + } \keyword{Analytical} \keyword{Merge} diff --git a/man/ToyData.Rd b/man/ToyData.Rd index b9acf8c..61e39bd 100644 --- a/man/ToyData.Rd +++ b/man/ToyData.Rd @@ -24,9 +24,9 @@ ToyData(Dataset) A data frame containing the toy data. } \description{ -Import and process .csv file to create toy data. +Import and process .csv file to create toy data DF. } \examples{ -Intra <- MetaProViz::ToyData("IntraCells_Raw") +Intra <- ToyData("IntraCells_Raw") } diff --git a/man/TranslateID.Rd b/man/TranslateID.Rd index 063efab..7ab92bd 100644 --- a/man/TranslateID.Rd +++ b/man/TranslateID.Rd @@ -1,27 +1,37 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/GetPriorKnoweldge.R +% Please edit documentation in R/RefactorPriorKnoweldge.R \name{TranslateID} \alias{TranslateID} -\title{Translate IDs} +\title{Translate IDs to/from KEGG, PubChem, Chebi, HMDB} \usage{ TranslateID( - Input_DataFrame, - SettingsInfo = list(IdColumn = "MetaboliteID", FromFormat = c("kegg"), ToFormat = - c("pubchem", "chebi", "hmdb"), Method = "GetAll", GroupingVariable = "term") + InputData, + SettingsInfo = c(InputID = "MetaboliteID", GroupingVariable = "term"), + From = c("kegg"), + To = c("pubchem", "chebi", "hmdb"), + SaveAs_Table = "csv", + FolderPath = NULL ) } \arguments{ -\item{Input_DataFrame}{Dataframe with two columns for source (=term) and Target (=gene), e.g. Hallmarks.} +\item{InputData}{Dataframe with at least one column with the target (e.g. metabolite), you can add other columns such as source (e.g. term)} -\item{SettingsInfo}{\emph{Optional: } Column name of Target in Input_GeneSet. \strong{Default = list(IdColumn="MetaboliteID", FromFormat=c("kegg"), ToFormat=c("pubchem","chebi","hmdb"), Method="GetAll", GroupingVariable="term")}} +\item{SettingsInfo}{\emph{Optional: } Column name of Target in Input_GeneSet. \strong{Default = list(InputID="MetaboliteID" , GroupingVariable="term")}} \item{SaveAs_Table}{\emph{Optional: } File types for the analysis results are: "csv", "xlsx", "txt". \strong{Default = "csv"}} \item{FolderPath}{{Optional:} String which is added to the resulting folder name \strong{Default = NULL}} } \value{ -3 data frames: 1) Original data and the new column of translated ids. 2) Mapping summary from Original ID to Translated. 3) Mapping summary from Translated to Original. +List with three DFs: 1) Original data and the new column of translated ids. 2) Mapping summary from Original ID to Translated. 3) Mapping summary from Translated to Original. } \description{ -Translate IDs to and from KEGG, PubChem, Chebi. +Translate IDs to/from KEGG, PubChem, Chebi, HMDB } +\examples{ +KEGG_Pathways <- MetaProViz::LoadKEGG() +res <- MetaProViz::TranslateID(InputData= KEGG_Pathways, SettingsInfo = c(InputID="MetaboliteID", GroupingVariable="term"), From = c("kegg"), To = c("pubchem","chebi","hmdb"), Method="GetAll", SaveAs_Table= "csv", FolderPath=NULL) + +} +\keyword{IDs} +\keyword{Translate} diff --git a/man/VizHeatmap.Rd b/man/VizHeatmap.Rd index 5724df2..1ce19c8 100644 --- a/man/VizHeatmap.Rd +++ b/man/VizHeatmap.Rd @@ -48,8 +48,8 @@ This script allows you to perform different data visualizations using the result Heatmap visualization } \examples{ -Intra <- MetaProViz::ToyData("IntraCells_Raw") -Res <- MetaProViz::VizHeatmap(InputData=Intra[,-c(1:3)]) +Intra <- ToyData("IntraCells_Raw") +Res <- VizHeatmap(InputData=Intra[,-c(1:3)]) } \keyword{Heatmap} diff --git a/man/VizPCA.Rd b/man/VizPCA.Rd index ed6f804..760d932 100644 --- a/man/VizPCA.Rd +++ b/man/VizPCA.Rd @@ -56,8 +56,8 @@ This script allows you to perform PCA plot visualization using the results of th PCA plot visualization } \examples{ -Intra <- MetaProViz::ToyData("IntraCells_Raw")[,-c(1:3)] -Res <- MetaProViz::VizPCA(Intra) +Intra <- ToyData("IntraCells_Raw")[,-c(1:3)] +Res <- VizPCA(Intra) } \keyword{PCA} diff --git a/man/VizSuperplot.Rd b/man/VizSuperplot.Rd index 0b88cb1..944b6f9 100644 --- a/man/VizSuperplot.Rd +++ b/man/VizSuperplot.Rd @@ -68,8 +68,8 @@ This script allows you to perform different visualizations (bar, box, violin plo Bar, Box or Violin plot in Superplot style visualization } \examples{ -Intra <- MetaProViz::ToyData("IntraCells_Raw")[,c(1:6)] -Res <- MetaProViz::VizSuperplot(InputData=Intra[,-c(1:3)], SettingsFile_Sample=Intra[,c(1:3)], SettingsInfo = c(Conditions="Conditions", Superplot = NULL)) +Intra <- ToyData("IntraCells_Raw")[,c(1:6)] +Res <- VizSuperplot(InputData=Intra[,-c(1:3)], SettingsFile_Sample=Intra[,c(1:3)], SettingsInfo = c(Conditions="Conditions", Superplot = NULL)) } \keyword{Barplot,} diff --git a/man/VizVolcano.Rd b/man/VizVolcano.Rd index f0832d7..5130f76 100644 --- a/man/VizVolcano.Rd +++ b/man/VizVolcano.Rd @@ -86,8 +86,8 @@ This script allows you to perform different data visualizations using the result Volcano plot visualization } \examples{ -Intra <- MetaProViz::ToyData("IntraCells_DMA") -Res <- MetaProViz::VizVolcano(InputData=Intra) +Intra <- ToyData("IntraCells_DMA") +Res <- VizVolcano(InputData=Intra) } \keyword{Volcano} diff --git a/man/metaproviz_log.Rd b/man/metaproviz_log.Rd deleted file mode 100644 index 8ea6047..0000000 --- a/man/metaproviz_log.Rd +++ /dev/null @@ -1,24 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/HelperLog.R -\name{MetaProViz_log} -\alias{MetaProViz_log} -\title{Browse the current MetaProViz log file} -\usage{ -MetaProViz_log() -} -\value{ -Returns \code{NULL}. -} -\description{ -Browse the current MetaProViz log file -} -\examples{ -\dontrun{ -metaproviz_log() -# then you can browse the log file, and exit with `q` -} - -} -\seealso{ -\code{\link{metaproviz_logfile}} -} diff --git a/man/metaproviz_logfile.Rd b/man/metaproviz_logfile.Rd deleted file mode 100644 index f4db981..0000000 --- a/man/metaproviz_logfile.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/HelperLog.R -\name{MetaProViz_logfile} -\alias{MetaProViz_logfile} -\title{Path to the current MetaProViz log file} -\usage{ -MetaProViz_logfile() -} -\value{ -Character: path to the current logfile, or \code{NULL} if no -logfile is available. -} -\description{ -Path to the current MetaProViz log file -} -\examples{ -metaproviz_logfile() -# [1] "path/metaproviz/metaproviz-log/metaproviz-20210309-1642.log" - -} -\seealso{ -\code{\link{metaproviz_log}} -} diff --git a/man/metaproviz_set_loglevel.Rd b/man/metaproviz_set_loglevel.Rd deleted file mode 100644 index 90be8bf..0000000 --- a/man/metaproviz_set_loglevel.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/HelperLog.R -\name{MetaProViz_set_loglevel} -\alias{MetaProViz_set_loglevel} -\title{Sets the log level for the package logger} -\usage{ -MetaProViz_set_loglevel(level, target = "logfile") -} -\arguments{ -\item{level}{Character or class \code{loglevel}. The desired log level.} - -\item{target}{Character, either 'logfile' or 'console'} -} -\value{ -Returns \code{NULL}. -} -\description{ -Sets the log level for the package logger -} -\examples{ -metaproviz_set_loglevel(logger::FATAL, target = 'console') - -}