Update documentation 3 - fixes

DESCRIPTION

@@ -31,7 +31,6 @@ Imports:
     magrittr,
     rlang,
     stats,
-    statmod,
     stringr,
     tidyr,
     utils

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)

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)

R/logRatioPlot.R

@@ -14,9 +14,9 @@
 #' ggplots, one for each facetColname value \emph{(typically gene)}.
 #'
 #' @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 (default = "Contrast").
+#' @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 (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")

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

R/obsPlot.R

@@ -13,24 +13,24 @@
 #'
 #' @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)
 #' @param showPoints Shows the data points on the plot (default = TRUE)
 #' @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)
 #'

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)

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.