Add plotting and other functions to evaluate mash results

DESCRIPTION

@@ -35,4 +35,5 @@ Imports:
     tidyr,
     tidyselect
 Suggests: 
+    dots,
     roxygen2

NAMESPACE

@@ -50,6 +50,7 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
 importFrom(dplyr,rename)
+importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,slice_max)
@@ -80,6 +81,7 @@ importFrom(stats,qbeta)
 importFrom(stats,uniroot)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
+importFrom(stringr,str_sub)
 importFrom(tibble,add_column)
 importFrom(tibble,add_row)
 importFrom(tibble,as_tibble)

man/check_covmat_basics.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/wrapper.R
+\name{check_covmat_basics}
+\alias{check_covmat_basics}
+\title{Basic sanity check for covariance matrices}
+\usage{
+check_covmat_basics(x)
+}
+\arguments{
+\item{x}{input matrix}
+}
+\description{
+Basic sanity check for covariance matrices
+}

man/check_positive_definite.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/wrapper.R
+\name{check_positive_definite}
+\alias{check_positive_definite}
+\title{check matrix for positive definitness}
+\usage{
+check_positive_definite(x)
+}
+\arguments{
+\item{x}{input matrix}
+}
+\description{
+check matrix for positive definitness
+}

man/labelled_stop.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/wrapper.R
+\name{labelled_stop}
+\alias{labelled_stop}
+\title{A wrapper function to \code{stop} call}
+\usage{
+labelled_stop(x, msg)
+}
+\arguments{
+\item{x}{input matrix}
+
+\item{msg}{Character string. A message to append to the stop call.}
+}
+\description{
+A wrapper function to \code{stop} call
+}

man/mash_plot_Ulist.Rd

@@ -23,7 +23,9 @@ mash_plot_Ulist(
 \item{suffix}{Character. Optional. A unique suffix used to save the files,
 instead of the current date & time.}
 
-\item{limits}{should there be plot limits of -1 and 1? Default is true.}
+\item{limits}{Logical. Should there be plot limits of -1 and 1? Default is TRUE.}
+
+\item{labels}{Logical. Should each pairwise comparison proportion have a label? Default is TRUE.}
 }
 \value{
 A list of dataframes used to make the tile plots and the plots

man/printf2.Rd

@@ -2,10 +2,15 @@
 % Please edit documentation in R/wrapper.R
 \name{printf2}
 \alias{printf2}
-\title{Verbose?}
+\title{print message function if verbose}
 \usage{
 printf2(verbose, ...)
 }
-\description{
+\arguments{
-Verbose?
+\item{verbose}{Logical. If TRUE, print progress messages.}
+
+\item{...}{Other arguments to \code{printf()}}
+}
+\description{
+print message function if verbose
 }