ococrook · ococrook · Feb 15, 2022 · Feb 15, 2022 · Feb 16, 2022 · Feb 16, 2022
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,18 +1,18 @@
 Package: hdxstats
 Title: Statistical analysis of hydrogen deuterium exchange mass spectrometry
-Version: 1.0
-Author: c(person("Crook", "Oliver M.",
-		    email = "oliver.crook@stats.ox.ac.uk",
-		    comment = c(ORCID = "0000-0001-5669-8506"),
-		    role = c("aut", "cre")))
-Maintainer: Oliver Crook <oliver.crook@stats.ox.ac.uk>
+Version: 1.0.1
+Authors@R: c(person(family = "Crook", given = "Oliver M.",
+		                email = "oliver.crook@stats.ox.ac.uk",
+		                comment = c(ORCID = "0000-0001-5669-8506"),
+		                role = c("aut", "cre")))
 Description: The hdxstats package enables the analysis and visualisation
     of hydrogen deuterium exchange mass spectromery experiments. It supports
-    of hydrogen deuterium exchange mass spectromery experiments. It supports
+    of hydrogen deuterium exchange mass spectrometry experiments. It supports
-    of hydrogen deuterium exchange mass spectromery experiments. It supports
+    of hydrogen deuterium exchange mass spectrometry experiments. It supports
     all types of HDX-MS experiments but provides additional support for epitope
-    mapping experiments. 
+    mapping experiments. The package focuses and implements empirical Bayes
+    functional models for hydrogen deuterium exchange data.
 License: Artistic-2.0
 Encoding: UTF-8
-Depends: R (>= 4.0), S4Vectors, Biobase, QFeatures
+Depends: R (>= 4.1), S4Vectors, Biobase, QFeatures
 Imports: Rcpp (>= 1.0.4.6),
     ggplot2,
     dplyr,
@@ -29,7 +29,8 @@ Imports: Rcpp (>= 1.0.4.6),
     broom,
     limma,
     lmerTest,
-    harmonicmeanp
+    harmonicmeanp,
+    stats
 Suggests: pheatmap,
     viridis,
     scales,

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,7 +9,11 @@ exportPattern("^[[:alpha:]]+")
     importFrom("minpack.lm", "nlsLM", "nls.lm.control")
     importFrom("broom", "tidy")
     importFrom("Biobase", "exprs")
-    importFrom("QFeatures", "readQFeatures")
+    importFrom("QFeatures", "readQFeatures", "longFormat")
     importFrom("S4Vectors", "DataFrame")
     importFrom("harmonicmeanp", "p.hmp")
+    importFrom("RColorBrewer", "brewer.pal")
+    importFrom("methods", "is")
+import("Rcpp", "ggplot2", "dplyr", "plyr", "knitr", "BiocParallel", "robustbase",
+       "BiocStyle", "stringi")    
 exportMethods(logLik, residuals, vcov, likRatio, coef, deviance, summary, wilk)
diff --git a/R/functionalAnalysis-plots.R b/R/functionalAnalysis-plots.R
@@ -693,7 +693,7 @@ forestPlot <- function(params, condition = c(1,2)) {
     model2 <- params@alternative@nlsmodels[[2]]
 
     tmp <- summary(model1)$parameters
-    tmp2 <- summary(model1)$parameters
+    tmp2 <- summary(model2)$parameters
 
     df <- data.frame(tmp)
     df$rownames <- rownames(df)
@@ -729,7 +729,7 @@ forestPlot <- function(params, condition = c(1,2)) {
         scale_color_viridis(discrete = TRUE, begin = 0.2, direction = 1) + theme(text = element_text(size = 16)) + 
         geom_vline(xintercept = 0, linetype = "dashed")
 
-    print(gg)
+    return(gg)
 }
 ##' Underlying computation for compute residue level differences plots. Uses
 ##' average differences at each residue. 

diff --git a/R/hdxstat-class.R b/R/hdxstat-class.R
@@ -32,7 +32,7 @@ setOldClass("gg")
 .hdxstatmodel <- setClass("HdxStatModel",
                           slots = c(nullmodel = "nls",
                                     alternative = "nlsList",
-                                    vis = "gg",
+                                    vis = "ANY",
                                     method = "character",
                                     formula = "formula"),
                           validity = function(object){

diff --git a/R/hdxstat-methods.R b/R/hdxstat-methods.R
@@ -66,6 +66,11 @@ setMethod("wilk", "HdxStatModel",
 setMethod("coef", "HdxStatModel",
           function(object) {
               .out <- t(sapply(c(list(object@nullmodel), object@alternative@nlsmodels), coef))
+              if(dim(.out)[1] == 1){
+                  nm <- colnames(.out)[1]
+                  .out <- t(.out)
+                  colnames(.out) <- nm
+              }
               rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))
-              if(dim(.out)[1] == 1){
-                  nm <- colnames(.out)[1]
-                  .out <- t(.out)
-                  colnames(.out) <- nm
-              }
-              rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))
+              if (dim(.out)[1] == 1) {
+                  ## Preserve all original column names as row names after transposing
+                  nm <- colnames(.out)
+                  .out <- t(.out)
+                  rownames(.out) <- nm
+              } else {
+                  rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))
+              }
-              if(dim(.out)[1] == 1){
-                  nm <- colnames(.out)[1]
-                  .out <- t(.out)
-                  colnames(.out) <- nm
-              }
-              rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))
+              if (dim(.out)[1] == 1) {
+                  ## Preserve all original column names as row names after transposing
+                  nm <- colnames(.out)
+                  .out <- t(.out)
+                  rownames(.out) <- nm
+              } else {
+                  rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))
+              }
               .out
           })

diff --git a/inst/extdata/Project_2_SecA_Cluster_Data.csv b/inst/extdata/Project_2_SecA_Cluster_Data.csv
diff --git a/vignettes/flexible-fits.html b/vignettes/flexible-fits.html