diff --git a/R/plotting.R b/R/plotting.R index 820446f..61d3b2b 100644 --- a/R/plotting.R +++ b/R/plotting.R @@ -192,7 +192,7 @@ plotClassifications <- function(classifications, name="classifications"){ nameClassifications=c("FN","FP","TN","TP") value <- unname(unlist(classificationsPerc[i,])) data <- data.frame(nameClassifications,value) - classPlot <- ggplot2::ggplot(data = data,ggplot2::aes(x=name,y=value))+ + classPlot <- ggplot2::ggplot(data = data,ggplot2::aes(x=nameClassifications,y=value))+ ggplot2::geom_bar(stat = "identity",fill= c("red4","firebrick2","limegreen","lawngreen"))+ ggplot2::scale_fill_manual(values = c("red4","firebrick2","limegreen","lawngreen"))+ ggplot2::theme_bw()+ggplot2::theme(legend.position = "none",plot.title = ggplot2::element_text(hjust = 0.5))+ diff --git a/bimodalR.Rproj b/bimodalR.Rproj deleted file mode 100644 index cba1b6b..0000000 --- a/bimodalR.Rproj +++ /dev/null @@ -1,21 +0,0 @@ -Version: 1.0 - -RestoreWorkspace: No -SaveWorkspace: No -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -AutoAppendNewline: Yes -StripTrailingWhitespace: Yes - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source -PackageRoxygenize: rd,collate,namespace diff --git a/vignettes/multimodalR.Rmd b/vignettes/multimodalR.Rmd index 096b835..f58c09c 100644 --- a/vignettes/multimodalR.Rmd +++ b/vignettes/multimodalR.Rmd @@ -644,7 +644,7 @@ If all of those requirements are fulfilled, the function should return 'TRUE', i ## Usage of the algorithms In this package three algorithms that can be used for detecting multimodality, -are implemented. +are implemented. The mclust algorithm that can be used with useMclust() is the one recommended to detect multimodal genes in gene expression data sets. ### mclust Mclust uses a finite Gaussian mixture modeling fitted via EM algorithm for @@ -754,7 +754,7 @@ To use the FlexMix algorithm on your expression data frame (simulated or not) and gain information which genes are bimodal use the useFlexmix() command: ```{r useFlexmix,eval = FALSE} #use FlexMix with the expression data frame expression -flexmixOutput <- useFlexmix(expression = expression,maxModality = 2,reps = 1) +flexmixOutput <- useFlexmix(expression = expression,maxModality = 2) ```