From 3fe41ee1fb31f4823960efcde4067e08e2b626f6 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Fri, 28 Jan 2022 16:36:52 -0800 Subject: [PATCH 01/11] make the package installation in R 4.0.5 and Latest the same --- .circleci/config.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6aa447ca..8705a2f0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -76,10 +76,8 @@ jobs: R -e 'install.packages("covr")' R -e 'install.packages("devtools")' R -e 'devtools::install_github("cb4ds/DGEobj.utils@cran")' - R -e 'install.packages("canvasXpress")' - R -e 'install.packages("ggrepel")' - R -e 'install.packages("igraph")' - R -e 'install.packages("statmod")' + R -e 'install.packages("remotes")' + R -e 'remotes::install_deps(dependencies = TRUE)' - run: name: Session information and installed package versions command: | From 77f8bec1e7e7e8c7fea759d71ae6be53537c7a78 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 31 Jan 2022 10:08:13 -0800 Subject: [PATCH 02/11] remove the install of DGEobj.utils@cran --- .circleci/config.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 8705a2f0..2e0f3963 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -27,8 +27,6 @@ jobs: R -e 'install.packages("BiocManager")' R -e 'BiocManager::install(c("limma", "edgeR"))' R -e 'install.packages("covr")' - R -e 'install.packages("devtools")' - R -e 'devtools::install_github("cb4ds/DGEobj.utils@cran")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' - run: @@ -74,8 +72,6 @@ jobs: R -e 'install.packages("BiocManager")' R -e 'BiocManager::install(c("limma", "edgeR"))' R -e 'install.packages("covr")' - R -e 'install.packages("devtools")' - R -e 'devtools::install_github("cb4ds/DGEobj.utils@cran")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' - run: From bc26d7618dfca2950bc86c97eb0c80f0a6b0743b Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 31 Jan 2022 10:18:31 -0800 Subject: [PATCH 03/11] install DGEobj and DGEobj.utils --- .circleci/config.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index 2e0f3963..35580e05 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -29,6 +29,8 @@ jobs: R -e 'install.packages("covr")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' + R -e 'install.packages("DGEobj")' + R -e 'install.packages("DGEobj.utils")' - run: name: Session information and installed package versions command: | @@ -74,6 +76,8 @@ jobs: R -e 'install.packages("covr")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' + R -e 'install.packages("DGEobj")' + R -e 'install.packages("DGEobj.utils")' - run: name: Session information and installed package versions command: | From 61cf62785f9299d7602389c61b6042046b3f5ed1 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 31 Jan 2022 11:09:40 -0800 Subject: [PATCH 04/11] add the bioconductor dependencies in DGEobj and DGEobj.utils --- .circleci/config.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 35580e05..86029c72 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -25,12 +25,10 @@ jobs: name: Install R dependencies command: | R -e 'install.packages("BiocManager")' - R -e 'BiocManager::install(c("limma", "edgeR"))' + R -e 'BiocManager::install(c("limma", "edgeR", "qvalue", "sva", "GenomicRanges"))' R -e 'install.packages("covr")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' - R -e 'install.packages("DGEobj")' - R -e 'install.packages("DGEobj.utils")' - run: name: Session information and installed package versions command: | @@ -72,12 +70,10 @@ jobs: name: Install R dependencies command: | R -e 'install.packages("BiocManager")' - R -e 'BiocManager::install(c("limma", "edgeR"))' + R -e 'BiocManager::install(c("limma", "edgeR", "qvalue", "sva", "GenomicRanges"))' R -e 'install.packages("covr")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' - R -e 'install.packages("DGEobj")' - R -e 'install.packages("DGEobj.utils")' - run: name: Session information and installed package versions command: | From 05e84ec17991e5f9018d4633e432c53c81142203 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 31 Jan 2022 11:22:21 -0800 Subject: [PATCH 05/11] add DGEObj.utils suggested bioconductor packages --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 86029c72..cc190869 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -70,7 +70,7 @@ jobs: name: Install R dependencies command: | R -e 'install.packages("BiocManager")' - R -e 'BiocManager::install(c("limma", "edgeR", "qvalue", "sva", "GenomicRanges"))' + R -e 'BiocManager::install(c("limma", "edgeR", "qvalue", "sva", "GenomicRanges", "zFPKM", "RNASeqPower", "IHW"))' R -e 'install.packages("covr")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' From 3c7d905315f0bd78be5335d504b535e15f5d904f Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 31 Jan 2022 11:26:01 -0800 Subject: [PATCH 06/11] install the suggested DGEobj.utils bioconductor packages on R 4.0.5 --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index cc190869..ef994c5f 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -25,7 +25,7 @@ jobs: name: Install R dependencies command: | R -e 'install.packages("BiocManager")' - R -e 'BiocManager::install(c("limma", "edgeR", "qvalue", "sva", "GenomicRanges"))' + R -e 'BiocManager::install(c("limma", "edgeR", "qvalue", "sva", "GenomicRanges", "zFPKM", "RNASeqPower", "IHW"))' R -e 'install.packages("covr")' R -e 'install.packages("remotes")' R -e 'remotes::install_deps(dependencies = TRUE)' From ff64b4a4e3eeea464aed57e5cd65dacce7161c91 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 31 Jan 2022 12:51:13 -0800 Subject: [PATCH 07/11] remove the mentions of required in the parameter documentation and note that labelAngle does not apply to histograms --- R/QCplots.R | 7 ++++--- R/cdfPlot.R | 4 ++-- R/comparePlot.R | 2 +- R/ggplotMDS.R | 4 ++-- R/logRatioPlot.R | 4 ++-- R/plotNorm.R | 2 +- R/plotPValHist.R | 2 +- R/profilePlot.R | 2 +- R/volcanoPlot.R | 2 +- man/MDS_var_explained.Rd | 2 +- man/QCplots.Rd | 7 ++++--- man/cdfPlot.Rd | 4 ++-- man/comparePrep.Rd | 2 +- man/ggplotMDS.Rd | 2 +- man/logRatioPlot.Rd | 4 ++-- man/plotNorm.Rd | 2 +- man/plotPvalHist.Rd | 2 +- man/profilePlot.Rd | 2 +- man/volcanoPlot.Rd | 2 +- 19 files changed, 30 insertions(+), 28 deletions(-) diff --git a/R/QCplots.R b/R/QCplots.R index 7be1101b..90f4bfb3 100644 --- a/R/QCplots.R +++ b/R/QCplots.R @@ -9,14 +9,15 @@ #' By default, horizontal reference lines are drawn at the median and +/- n SDs based on the #' hlineSD argument. These are statistical reference points, NOT pass/fail limits. #' -#' @param DGEdata A DGEobj object with an item of type "alignQC" (required) +#' @param DGEdata A DGEobj object with an item of type "alignQC" #' @param metricNames A list of metrics to plot. Values must exist in column names of the item -#' of type AlignQC. (required) +#' of type AlignQC. #' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress). #' @param plotCategory One of "bar", "point", "pointline" or "histogram". For a different #' plot type for each metric, pass a list of plotCategories with length equal to #' length(metricNames). (default = "bar") -#' @param labelAngle Angle (0 - 90) to set the sample labels on the X axis (default = 30) +#' @param labelAngle Angle (0 - 90) to set the sample labels on the X axis (default = 30). +#' Does not apply to histograms. #' @param hlineSD Draw two reference lines: 1) at the median value 2) the number of #' SDs defined by the value of hlineSD. (default = 3). Set to 0 to disable the reference lines. #' @param winsorize This implements a robust method to calculate standard diff --git a/R/cdfPlot.R b/R/cdfPlot.R index c7117365..0464a3e9 100644 --- a/R/cdfPlot.R +++ b/R/cdfPlot.R @@ -12,8 +12,8 @@ #' the second plot (all_pval) shows all the p-values. For plotType ="ggplot", output also #' contains an additional plot that displays the all_pval plot as an inset in below_pvalMax. #' -#' @param dgeObj A DGEobj with one or more topTables (required) -#' @param contrast Name of a topTable dataframe with p-value or an FDR column (required) +#' @param dgeObj A DGEobj with one or more topTables +#' @param contrast Name of a topTable dataframe with p-value or an FDR column #' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress). #' @param pvalCol Name of the p-value or FDR column (default = "P.Value") #' @param pvalMax Limit the range of the main plot (default = 0.10) diff --git a/R/comparePlot.R b/R/comparePlot.R index 9cc854de..9440e6fb 100644 --- a/R/comparePlot.R +++ b/R/comparePlot.R @@ -333,7 +333,7 @@ comparePlot <- function(dgeObj, #' (present in both datasets). The two dataframes must have the same type of #' gene IDs as rownames. #' -#' @param contrastList A named list of 2 topTable dataframes (required). The +#' @param contrastList A named list of 2 topTable dataframes. The #' names are used as column names for the value columns in the output. #' @param valueCol Name of column containing values to plot (default = "logFC") #' @param significanceCol Name of column to use for significance (default = "P.Value") diff --git a/R/ggplotMDS.R b/R/ggplotMDS.R index 9beb8a02..c4986b6d 100644 --- a/R/ggplotMDS.R +++ b/R/ggplotMDS.R @@ -13,7 +13,7 @@ #' allows for selection of a number close the number of differential genes in the #' input data. #' -#' @param dgeObj A DGEobj object with a DGEList and design table (required) +#' @param dgeObj A DGEobj object with a DGEList and design table #' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress) #' @param designTable Name of the design table object (default = design) #' @param colorBy A column name in the design table. Points are colored by the values in that column (default = ReplicateGroup) @@ -450,7 +450,7 @@ ggplotMDS <- function(dgeObj, #' it plots the first 10 dimensions or the first N dimensions totaling 90%. #' #' @param mds A class MDS object from limma::plotMDS() or a data matrix to analyze -#' (typically log2) (required) +#' (typically log2) #' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress). #' @param topN The number of dimensions to plot (default = 10) #' @param cumVarLimit The maximum cumulative variance to plot. Range 0-1. (default = 0.9) diff --git a/R/logRatioPlot.R b/R/logRatioPlot.R index f62f3fdf..26f02f6b 100644 --- a/R/logRatioPlot.R +++ b/R/logRatioPlot.R @@ -13,10 +13,10 @@ #' If \code{facet} parameter is set to \strong{FALSE} the output will be a list of individual canvasXpress or #' ggplots, one for each facetColname value \emph{(typically gene)}. #' -#' @param dgeObj A DGEobj that contains topTable objects (required) +#' @param dgeObj A DGEobj that contains topTable objects #' @param plotType Plot type must be canvasXpress or ggplot (default to canvasXpress). #' @param facetColname Column name to separate plots from geneData (default = "rgd_symbol"). -#' @param xColname The computed column to group boxplots by (required) (default = "Contrast"). +#' @param xColname The computed column to group boxplots by (default = "Contrast"). #' @param yColname Column name for the output of the boxplots (default = "logFC") #' @param CI.R_colname Name of the CI high value (default = "CI.R") #' @param CI.L_colname Name of the CI low value (default = "CI.L") diff --git a/R/plotNorm.R b/R/plotNorm.R index 9939192c..0821ed7a 100644 --- a/R/plotNorm.R +++ b/R/plotNorm.R @@ -8,7 +8,7 @@ #' Normalization is performed by edgeR::calcNormFactors. Note TMM is specifically tailored for count-based #' data. Thus this function is only appropriate for count-based data. #' -#' @param dgeObj DGEobj with a counts Matrix (required) +#' @param dgeObj DGEobj with a counts Matrix #' @param plotType Plot type must be canvasXpress or ggplot (defaults to canvasXpress). #' @param plotCategory Show a "box" or "density" plot (default = "box") #' @param normalize The type of normalization to use (default = "TMM"). Other allowed diff --git a/R/plotPValHist.R b/R/plotPValHist.R index dded9c72..1e994d22 100644 --- a/R/plotPValHist.R +++ b/R/plotPValHist.R @@ -4,7 +4,7 @@ #' numbers. Intended to perform histogram analysis of p-value distributions, #' but should be useful for any dataframe of numeric columns. #' -#' @param dgeObj DGEobj with topTables (required) +#' @param dgeObj DGEobj with topTables #' @param P.Val p-value column name in the topTables in DGEobj (default = "P.Value") #' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress). #' @param facet Set to FALSE to print individual plots instead of a faceted plot (default = TRUE) diff --git a/R/profilePlot.R b/R/profilePlot.R index 0491eba8..3f3c35b0 100644 --- a/R/profilePlot.R +++ b/R/profilePlot.R @@ -25,7 +25,7 @@ #' A significance measure (which defaults to P.Value <= 0.01) is used to color code genes that #' are significantly increased or decreased. # -#' @param dgeObj DGEobj with a topTable itemType (required). +#' @param dgeObj DGEobj with a topTable itemType. #' @param contrast itemName of the contrast in the dgeObj. #' @param plotType Plot type must be canvasXpress or ggplot (default = "canvasXpress"). #' @param logRatioCol Name of the LogRatio column (default = "logFC") diff --git a/R/volcanoPlot.R b/R/volcanoPlot.R index a486fdfb..78eb8564 100644 --- a/R/volcanoPlot.R +++ b/R/volcanoPlot.R @@ -22,7 +22,7 @@ #' threshold are used to color code genes that are significantly increased or decreased. #' Use the appropriate arguments to use an FDR measure instead of p-value. #' -#' @param dgeObj DGEobj with a topTable dataframe (required) +#' @param dgeObj DGEobj with a topTable dataframe #' @param contrast Name of the contrast #' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress) #' @param logRatioCol Name of the LogRatio column (default = "logFC") diff --git a/man/MDS_var_explained.Rd b/man/MDS_var_explained.Rd index 716683d6..51ece9d7 100644 --- a/man/MDS_var_explained.Rd +++ b/man/MDS_var_explained.Rd @@ -15,7 +15,7 @@ MDS_var_explained( } \arguments{ \item{mds}{A class MDS object from limma::plotMDS() or a data matrix to analyze -(typically log2) (required)} +(typically log2)} \item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress).} diff --git a/man/QCplots.Rd b/man/QCplots.Rd index b0c248e7..c86d0675 100644 --- a/man/QCplots.Rd +++ b/man/QCplots.Rd @@ -15,10 +15,10 @@ QCplots( ) } \arguments{ -\item{DGEdata}{A DGEobj object with an item of type "alignQC" (required)} +\item{DGEdata}{A DGEobj object with an item of type "alignQC"} \item{metricNames}{A list of metrics to plot. Values must exist in column names of the item -of type AlignQC. (required)} +of type AlignQC.} \item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress).} @@ -26,7 +26,8 @@ of type AlignQC. (required)} plot type for each metric, pass a list of plotCategories with length equal to length(metricNames). (default = "bar")} -\item{labelAngle}{Angle (0 - 90) to set the sample labels on the X axis (default = 30)} +\item{labelAngle}{Angle (0 - 90) to set the sample labels on the X axis (default = 30). +Does not apply to histograms.} \item{hlineSD}{Draw two reference lines: 1) at the median value 2) the number of SDs defined by the value of hlineSD. (default = 3). Set to 0 to disable the reference lines.} diff --git a/man/cdfPlot.Rd b/man/cdfPlot.Rd index 3dc9c974..33a0c8be 100644 --- a/man/cdfPlot.Rd +++ b/man/cdfPlot.Rd @@ -22,9 +22,9 @@ cdfPlot( ) } \arguments{ -\item{dgeObj}{A DGEobj with one or more topTables (required)} +\item{dgeObj}{A DGEobj with one or more topTables} -\item{contrast}{Name of a topTable dataframe with p-value or an FDR column (required)} +\item{contrast}{Name of a topTable dataframe with p-value or an FDR column} \item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress).} diff --git a/man/comparePrep.Rd b/man/comparePrep.Rd index 1d403a0c..c69070fb 100644 --- a/man/comparePrep.Rd +++ b/man/comparePrep.Rd @@ -7,7 +7,7 @@ comparePrep(contrastList, valueCol = "logFC", significanceCol = "P.Value") } \arguments{ -\item{contrastList}{A named list of 2 topTable dataframes (required). The +\item{contrastList}{A named list of 2 topTable dataframes. The names are used as column names for the value columns in the output.} \item{valueCol}{Name of column containing values to plot (default = "logFC")} diff --git a/man/ggplotMDS.Rd b/man/ggplotMDS.Rd index 194d92f3..03d30a7f 100644 --- a/man/ggplotMDS.Rd +++ b/man/ggplotMDS.Rd @@ -21,7 +21,7 @@ ggplotMDS( ) } \arguments{ -\item{dgeObj}{A DGEobj object with a DGEList and design table (required)} +\item{dgeObj}{A DGEobj object with a DGEList and design table} \item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress)} diff --git a/man/logRatioPlot.Rd b/man/logRatioPlot.Rd index 0759fc1d..9df246f3 100644 --- a/man/logRatioPlot.Rd +++ b/man/logRatioPlot.Rd @@ -23,13 +23,13 @@ logRatioPlot( ) } \arguments{ -\item{dgeObj}{A DGEobj that contains topTable objects (required)} +\item{dgeObj}{A DGEobj that contains topTable objects} \item{plotType}{Plot type must be canvasXpress or ggplot (default to canvasXpress).} \item{facetColname}{Column name to separate plots from geneData (default = "rgd_symbol").} -\item{xColname}{The computed column to group boxplots by (required) (default = "Contrast").} +\item{xColname}{The computed column to group boxplots by (default = "Contrast").} \item{yColname}{Column name for the output of the boxplots (default = "logFC")} diff --git a/man/plotNorm.Rd b/man/plotNorm.Rd index 3067bb2d..de7af387 100644 --- a/man/plotNorm.Rd +++ b/man/plotNorm.Rd @@ -12,7 +12,7 @@ plotNorm( ) } \arguments{ -\item{dgeObj}{DGEobj with a counts Matrix (required)} +\item{dgeObj}{DGEobj with a counts Matrix} \item{plotType}{Plot type must be canvasXpress or ggplot (defaults to canvasXpress).} diff --git a/man/plotPvalHist.Rd b/man/plotPvalHist.Rd index c2913361..73134f19 100644 --- a/man/plotPvalHist.Rd +++ b/man/plotPvalHist.Rd @@ -13,7 +13,7 @@ plotPvalHist( ) } \arguments{ -\item{dgeObj}{DGEobj with topTables (required)} +\item{dgeObj}{DGEobj with topTables} \item{P.Val}{p-value column name in the topTables in DGEobj (default = "P.Value")} diff --git a/man/profilePlot.Rd b/man/profilePlot.Rd index 375a9979..082cec88 100644 --- a/man/profilePlot.Rd +++ b/man/profilePlot.Rd @@ -23,7 +23,7 @@ profilePlot( ) } \arguments{ -\item{dgeObj}{DGEobj with a topTable itemType (required).} +\item{dgeObj}{DGEobj with a topTable itemType.} \item{contrast}{itemName of the contrast in the dgeObj.} diff --git a/man/volcanoPlot.Rd b/man/volcanoPlot.Rd index 16c26020..aec0d500 100644 --- a/man/volcanoPlot.Rd +++ b/man/volcanoPlot.Rd @@ -22,7 +22,7 @@ volcanoPlot( ) } \arguments{ -\item{dgeObj}{DGEobj with a topTable dataframe (required)} +\item{dgeObj}{DGEobj with a topTable dataframe} \item{contrast}{Name of the contrast} From 5c1794a770e598dc2444e8b64f80dc72eef73909 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Tue, 1 Feb 2022 12:05:48 -0800 Subject: [PATCH 08/11] remove the use of %$% --- R/ggplotMDS.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/ggplotMDS.R b/R/ggplotMDS.R index c4986b6d..a24d677a 100644 --- a/R/ggplotMDS.R +++ b/R/ggplotMDS.R @@ -527,10 +527,10 @@ MDS_var_explained <- function(mds, mds.distances <- tryCatch( expr = { - mds %$% distance.matrix %>% as.dist + as.dist(mds$distance.matrix) }, error = function(e) { - mds %$% distance.matrix.squared %>% as.dist + as.dist(mds$distance.matrix.squared) } ) From f878fd1b5922d2caacc76951e09c4f95796d49a0 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Mon, 14 Feb 2022 16:16:14 -0800 Subject: [PATCH 09/11] clean up documentation text --- R/cdfPlot.R | 2 +- R/ggplotMDS.R | 4 ++-- R/logRatioPlot.R | 2 +- R/mapDGEobj.R | 8 ++++---- R/obsPlot.R | 18 +++++++++--------- R/plotDispersion.R | 4 ++-- R/plotNorm.R | 2 +- 7 files changed, 20 insertions(+), 20 deletions(-) diff --git a/R/cdfPlot.R b/R/cdfPlot.R index 0464a3e9..740962c3 100644 --- a/R/cdfPlot.R +++ b/R/cdfPlot.R @@ -14,7 +14,7 @@ #' #' @param dgeObj A DGEobj with one or more topTables #' @param contrast Name of a topTable dataframe with p-value or an FDR column -#' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress). +#' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress) #' @param pvalCol Name of the p-value or FDR column (default = "P.Value") #' @param pvalMax Limit the range of the main plot (default = 0.10) #' @param pThreshold Significant value threshold (default = 0.01) diff --git a/R/ggplotMDS.R b/R/ggplotMDS.R index a24d677a..a0a17be5 100644 --- a/R/ggplotMDS.R +++ b/R/ggplotMDS.R @@ -23,8 +23,8 @@ #' @param labels A column name in the design table. Text labels for the samples. These should be short #' abbreviations of the sample identifiers. #' Default = ReplicateGroup or rownames of dgeObj. Set to NULL to disable -#' text labels. -#' @param title A title for the plot. (Optional) +#' text labels +#' @param title A title for the plot (Optional) #' @param xlab x axis label (Optional) #' @param ylab y axis label (Optional) #' @param vlineIntercept X intercept of vertical line (Optional) diff --git a/R/logRatioPlot.R b/R/logRatioPlot.R index 26f02f6b..934a1f62 100644 --- a/R/logRatioPlot.R +++ b/R/logRatioPlot.R @@ -15,7 +15,7 @@ #' #' @param dgeObj A DGEobj that contains topTable objects #' @param plotType Plot type must be canvasXpress or ggplot (default to canvasXpress). -#' @param facetColname Column name to separate plots from geneData (default = "rgd_symbol"). +#' @param facetColname Column name to separate plots from geneData (default = "rgd_symbol") #' @param xColname The computed column to group boxplots by (default = "Contrast"). #' @param yColname Column name for the output of the boxplots (default = "logFC") #' @param CI.R_colname Name of the CI high value (default = "CI.R") diff --git a/R/mapDGEobj.R b/R/mapDGEobj.R index e93fe886..0efd0126 100644 --- a/R/mapDGEobj.R +++ b/R/mapDGEobj.R @@ -3,12 +3,12 @@ #' Reads a DGEobj and visualizes parent/child relationships between #' data items in a DGEobj. #' -#' @param dgeObj DGEobj to find the parent/child relationships between data items. -#' @param plotType Must be canvasXpress or ggplot (default = canvasXpress). +#' @param dgeObj DGEobj to find the parent/child relationships between data items +#' @param plotType Must be canvasXpress or ggplot (default = canvasXpress) #' @param directed Only applies to ggplot. Indicates if the graph should -#' be directed or not. (default = TRUE) +#' be directed or not (default = TRUE) #' -#' @return A class ggplot object or a canvasXpress network plot. +#' @return A class ggplot object or a canvasXpress network plot #' #' #' @examples diff --git a/R/obsPlot.R b/R/obsPlot.R index a9a8e08e..12fc39e1 100644 --- a/R/obsPlot.R +++ b/R/obsPlot.R @@ -13,15 +13,15 @@ #' #' @param dgeObj A DGEObject. The countsMatrix in the DGEObject is extracted to plot the data. (required) #' @param plotType Can be canvasXpress or ggplot (default = canvasXpress) -#' @param designTable Name of the design table in the DGEObj from which the grouping column will be extracted. (default = design) -#' @param countsMatrix Name of the counts matrix in the DGEObj which will be used to render the plot.(default = counts) +#' @param designTable Name of the design table in the DGEObj from which the grouping column will be extracted (default = design) +#' @param countsMatrix Name of the counts matrix in the DGEObj which will be used to render the plot (default = counts) #' @param convertCounts A flag to indicate if counts matrix need to be converted or taken as is. Default value is NULL. This indicates -#' countsMatrix need to be taken as is. To convert the counts matrix, specify the desired unit. Supported units include CPM,FPKM, FPK and TPM. +#' countsMatrix need to be taken as is. To convert the counts matrix, specify the desired unit. Supported units include CPM, FPKM, FPK and TPM. #' This parameter is passed to DGEobj.utils::convertCounts (default = NULL) -#' @param convert_geneLength Parameter to pass to DGEobj.utils::convertCounts. (optional). -#' @param convert_log Parameter to pass to DGEobj.utils::convertCounts. (default = FALSE) -#' @param convert_normalize Parameter to pass to DGEobj.utils::convertCounts. (default = none) -#' @param convert_prior.count Parameter to pass to DGEobj.utils::convertCounts. (default = NULL) +#' @param convert_geneLength Parameter to pass to DGEobj.utils::convertCounts (optional) +#' @param convert_log Parameter to pass to DGEobj.utils::convertCounts (default = FALSE) +#' @param convert_normalize Parameter to pass to DGEobj.utils::convertCounts (default = none) +#' @param convert_prior.count Parameter to pass to DGEobj.utils::convertCounts (default = NULL) #' @seealso \link[DGEobj.utils]{convertCounts} #' @param group Define the column name to group boxplots by (typically a replicate group column) (required) #' @param violinLayer Adds a violin layer (default = FALSE) @@ -29,8 +29,8 @@ #' @param xlab X axis label (defaults to group column name if not specified) #' @param ylab Y axis label (defaults to value column name if not specified) #' @param title Plot title (optional) -#' @param facet Specifies whether to facet (TRUE) or print individual plots -#' (FALSE) (default = TRUE). It is recommended to facet no more than 40 plots. If 40 of more plots are needed, please set this argument to FALSE +#' @param facet Specifies whether to facet (TRUE, default) or print individual plots +#' (FALSE). It is recommended to facet no more than 40 plots. If 40 of more plots are needed, please set this argument to FALSE #' @param axisFree Specify same scale or independent scales for each subplot (default = TRUE; #' Allowed values: TRUE or FALSE) #' diff --git a/R/plotDispersion.R b/R/plotDispersion.R index f7fa1171..fb025d9c 100644 --- a/R/plotDispersion.R +++ b/R/plotDispersion.R @@ -7,8 +7,8 @@ #' #' @param dgeObj DGEobj which has a counts matrix or a DGElist #' @param replicateGroupCol A singular value of class character and must be a column name in design object (default = "ReplicateGroup") -#' @param countsMatrix If TRUE, uses the countsMatrix in DGEobj to construct the plot else DGElist will be used. (default = TRUE) -#' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress). +#' @param countsMatrix If TRUE, uses the countsMatrix in DGEobj to construct the plot else DGElist will be used (default = TRUE) +#' @param plotType Plot type must be canvasXpress or ggplot (default = canvasXpress) #' @param plotCategory One of "dispersion" or "BCV" (default = "dispersion") #' @param lineFit If the plotType is ggplot, any method supported by `geom_smooth()`. If the plotType is canvasXpress, one of glm, lm, loess, gam is accepted . #' Loess is recommended. (default = NULL) diff --git a/R/plotNorm.R b/R/plotNorm.R index 0821ed7a..14170543 100644 --- a/R/plotNorm.R +++ b/R/plotNorm.R @@ -10,7 +10,7 @@ #' #' @param dgeObj DGEobj with a counts Matrix #' @param plotType Plot type must be canvasXpress or ggplot (defaults to canvasXpress). -#' @param plotCategory Show a "box" or "density" plot (default = "box") +#' @param plotCategory Show a "box" or "density" plot (default = "box"). #' @param normalize The type of normalization to use (default = "TMM"). Other allowed #' values are: "RLE", "upperquartile" and "none". Invokes edgeR::calcNormFactors for #' normalization. From fb253a9911a1493fb93b198c89db0c0b4b51d576 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Tue, 22 Feb 2022 12:53:31 -0800 Subject: [PATCH 10/11] update manual files --- man/cdfPlot.Rd | 2 +- man/ggplotMDS.Rd | 4 ++-- man/logRatioPlot.Rd | 6 +++--- man/mapDGEobj.Rd | 8 ++++---- man/obsPlot.Rd | 18 +++++++++--------- man/plotDispersion.Rd | 4 ++-- man/plotNorm.Rd | 2 +- 7 files changed, 22 insertions(+), 22 deletions(-) diff --git a/man/cdfPlot.Rd b/man/cdfPlot.Rd index 33a0c8be..993f469a 100644 --- a/man/cdfPlot.Rd +++ b/man/cdfPlot.Rd @@ -26,7 +26,7 @@ cdfPlot( \item{contrast}{Name of a topTable dataframe with p-value or an FDR column} -\item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress).} +\item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress)} \item{pvalCol}{Name of the p-value or FDR column (default = "P.Value")} diff --git a/man/ggplotMDS.Rd b/man/ggplotMDS.Rd index 03d30a7f..2e52fa53 100644 --- a/man/ggplotMDS.Rd +++ b/man/ggplotMDS.Rd @@ -38,9 +38,9 @@ ggplotMDS( \item{labels}{A column name in the design table. Text labels for the samples. These should be short abbreviations of the sample identifiers. Default = ReplicateGroup or rownames of dgeObj. Set to NULL to disable -text labels.} +text labels} -\item{title}{A title for the plot. (Optional)} +\item{title}{A title for the plot (Optional)} \item{xlab}{x axis label (Optional)} diff --git a/man/logRatioPlot.Rd b/man/logRatioPlot.Rd index 9df246f3..6b981363 100644 --- a/man/logRatioPlot.Rd +++ b/man/logRatioPlot.Rd @@ -25,11 +25,11 @@ logRatioPlot( \arguments{ \item{dgeObj}{A DGEobj that contains topTable objects} -\item{plotType}{Plot type must be canvasXpress or ggplot (default to canvasXpress).} +\item{plotType}{Plot type must be canvasXpress or ggplot (default to canvasXpress)} -\item{facetColname}{Column name to separate plots from geneData (default = "rgd_symbol").} +\item{facetColname}{Column name to separate plots from geneData (default = "rgd_symbol")} -\item{xColname}{The computed column to group boxplots by (default = "Contrast").} +\item{xColname}{The computed column to group boxplots by (default = "Contrast")} \item{yColname}{Column name for the output of the boxplots (default = "logFC")} diff --git a/man/mapDGEobj.Rd b/man/mapDGEobj.Rd index e3de2373..87bf4c44 100644 --- a/man/mapDGEobj.Rd +++ b/man/mapDGEobj.Rd @@ -7,15 +7,15 @@ mapDGEobj(dgeObj, plotType = "canvasXpress", directed = TRUE) } \arguments{ -\item{dgeObj}{DGEobj to find the parent/child relationships between data items.} +\item{dgeObj}{DGEobj to find the parent/child relationships between data items} -\item{plotType}{Must be canvasXpress or ggplot (default = canvasXpress).} +\item{plotType}{Must be canvasXpress or ggplot (default = canvasXpress)} \item{directed}{Only applies to ggplot. Indicates if the graph should -be directed or not. (default = TRUE)} +be directed or not (default = TRUE)} } \value{ -A class ggplot object or a canvasXpress network plot. +A class ggplot object or a canvasXpress network plot } \description{ Reads a DGEobj and visualizes parent/child relationships between diff --git a/man/obsPlot.Rd b/man/obsPlot.Rd index 6cf9728d..e0e04b37 100644 --- a/man/obsPlot.Rd +++ b/man/obsPlot.Rd @@ -29,21 +29,21 @@ obsPlot( \item{plotType}{Can be canvasXpress or ggplot (default = canvasXpress)} -\item{countsMatrix}{Name of the counts matrix in the DGEObj which will be used to render the plot.(default = counts)} +\item{countsMatrix}{Name of the counts matrix in the DGEObj which will be used to render the plot (default = counts)} \item{convertCounts}{A flag to indicate if counts matrix need to be converted or taken as is. Default value is NULL. This indicates -countsMatrix need to be taken as is. To convert the counts matrix, specify the desired unit. Supported units include CPM,FPKM, FPK and TPM. +countsMatrix need to be taken as is. To convert the counts matrix, specify the desired unit. Supported units include CPM, FPKM, FPK and TPM. This parameter is passed to DGEobj.utils::convertCounts (default = NULL)} -\item{convert_geneLength}{Parameter to pass to DGEobj.utils::convertCounts. (optional).} +\item{convert_geneLength}{Parameter to pass to DGEobj.utils::convertCounts (optional)} -\item{convert_log}{Parameter to pass to DGEobj.utils::convertCounts. (default = FALSE)} +\item{convert_log}{Parameter to pass to DGEobj.utils::convertCounts (default = FALSE)} -\item{convert_normalize}{Parameter to pass to DGEobj.utils::convertCounts. (default = none)} +\item{convert_normalize}{Parameter to pass to DGEobj.utils::convertCounts (default = none)} -\item{convert_prior.count}{Parameter to pass to DGEobj.utils::convertCounts. (default = NULL)} +\item{convert_prior.count}{Parameter to pass to DGEobj.utils::convertCounts (default = NULL)} -\item{designTable}{Name of the design table in the DGEObj from which the grouping column will be extracted. (default = design)} +\item{designTable}{Name of the design table in the DGEObj from which the grouping column will be extracted (default = design)} \item{group}{Define the column name to group boxplots by (typically a replicate group column) (required)} @@ -57,8 +57,8 @@ This parameter is passed to DGEobj.utils::convertCounts (default = NULL)} \item{title}{Plot title (optional)} -\item{facet}{Specifies whether to facet (TRUE) or print individual plots -(FALSE) (default = TRUE). It is recommended to facet no more than 40 plots. If 40 of more plots are needed, please set this argument to FALSE} +\item{facet}{Specifies whether to facet (TRUE, default) or print individual plots +(FALSE). It is recommended to facet no more than 40 plots. If 40 of more plots are needed, please set this argument to FALSE} \item{axisFree}{Specify same scale or independent scales for each subplot (default = TRUE; Allowed values: TRUE or FALSE)} diff --git a/man/plotDispersion.Rd b/man/plotDispersion.Rd index 47eb6cda..532e953f 100644 --- a/man/plotDispersion.Rd +++ b/man/plotDispersion.Rd @@ -17,11 +17,11 @@ plotDispersion( \arguments{ \item{dgeObj}{DGEobj which has a counts matrix or a DGElist} -\item{countsMatrix}{If TRUE, uses the countsMatrix in DGEobj to construct the plot else DGElist will be used. (default = TRUE)} +\item{countsMatrix}{If TRUE, uses the countsMatrix in DGEobj to construct the plot else DGElist will be used (default = TRUE)} \item{replicateGroupCol}{A singular value of class character and must be a column name in design object (default = "ReplicateGroup")} -\item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress).} +\item{plotType}{Plot type must be canvasXpress or ggplot (default = canvasXpress)} \item{plotCategory}{One of "dispersion" or "BCV" (default = "dispersion")} diff --git a/man/plotNorm.Rd b/man/plotNorm.Rd index de7af387..54bd5137 100644 --- a/man/plotNorm.Rd +++ b/man/plotNorm.Rd @@ -16,7 +16,7 @@ plotNorm( \item{plotType}{Plot type must be canvasXpress or ggplot (defaults to canvasXpress).} -\item{plotCategory}{Show a "box" or "density" plot (default = "box")} +\item{plotCategory}{Show a "box" or "density" plot (default = "box").} \item{normalize}{The type of normalization to use (default = "TMM"). Other allowed values are: "RLE", "upperquartile" and "none". Invokes edgeR::calcNormFactors for From a3deb5fce1beed51b2755d2eb4b5897c0aab5199 Mon Sep 17 00:00:00 2001 From: Jasmine Lai Date: Tue, 22 Feb 2022 12:55:27 -0800 Subject: [PATCH 11/11] remove the duplicated statmod --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1dd61a4e..bc3446ad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -31,7 +31,6 @@ Imports: magrittr, rlang, stats, - statmod, stringr, tidyr, utils