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@@ -40,7 +40,9 @@
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#'
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#' pcaExplorer() # and then upload count matrix, covariate matrix (and eventual annotation)
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#' }
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-#'
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+#'
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+#' @importFrom mosdef gene_plot
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+#'
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#' @export
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pcaExplorer <- function(dds = NULL,
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dst = NULL,
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...
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@@ -1723,48 +1725,35 @@ pcaExplorer <- function(dds = NULL,
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1723
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1725
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1724
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1726
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genedata$sampleID <- rownames(genedata)
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1725
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1727
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1726
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- # input$plot_style chooses the style of plotting
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1727
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1728
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if (input$plot_style == "boxplot") {
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1728
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- res <- ggplot(genedata, aes_string(x = "plotby", y = "count", fill = "plotby")) +
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1729
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- geom_boxplot(outlier.shape = NA, alpha=0.7) + theme_bw()
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1730
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- if (input$ylimZero_genes) {
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1731
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))
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1732
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- } else {
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1733
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale")
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1734
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- }
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1735
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-
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1736
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- res <- res +
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1737
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- labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +
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1738
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- scale_x_discrete(name = "") +
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1739
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- geom_jitter(aes_string(x = "plotby", y = "count"), position = position_jitter(width = 0.1)) +
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1740
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- scale_fill_discrete(name = "Experimental\nconditions")
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1741
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- # if(input$addsamplelabels){
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1742
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- # res <- res + geom_text(aes(label=sampleID),hjust=-.1,vjust=0)
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1743
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- # }
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1744
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-
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1745
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- exportPlots$genesBoxplot <- res
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1746
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- res
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1747
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- } else if (input$plot_style == "violin plot"){
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1748
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- res <- ggplot(genedata, aes_string(x = "plotby", y = "count", fill = "plotby")) +
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1749
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- geom_violin(aes_string(col = "plotby"), alpha = 0.6) + theme_bw()
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1750
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- if (input$ylimZero_genes){
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1751
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))
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1752
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- } else {
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1753
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale")
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1754
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- }
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1755
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-
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1756
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- res <- res +
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1757
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- labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +
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- scale_x_discrete(name = "") +
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- geom_jitter(aes_string(x = "plotby", y = "count"), alpha = 0.8, position = position_jitter(width = 0.1)) +
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1760
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- scale_fill_discrete(name = "Experimental\nconditions") + scale_color_discrete(guide = "none")
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- # if(input$addsamplelabels){
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1762
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- # res <- res + geom_text(aes(label=sampleID),hjust=-.1,vjust=0)
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- # }
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1764
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-
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- exportPlots$genesBoxplot <- res
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1766
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- res
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+ plot_style <- "boxplot"
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+ } else if (input$plot_style == "violin plot") {
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+ plot_style <- "violin"
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+ } else {
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+ plot_style <- "auto"
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+ }
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+
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+ res <- mosdef::gene_plot(de_container = values$mydds,
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+ gene = selectedGene,
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+ intgroup = input$color_by,
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+ annotation_obj = values$myannotation,
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+ normalized = TRUE,
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+ plot_type = plot_style)
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+
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+ if (input$ylimZero_genes) {
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+ res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))
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+ } else {
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+ res <- res + scale_y_log10(name = "Normalized counts - log10 scale")
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}
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1748
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+
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+ res <- res +
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1750
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+ labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +
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1751
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+ scale_x_discrete(name = "") +
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1752
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+ scale_fill_discrete(name = "Experimental\nconditions")
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1753
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+
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1754
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+ exportPlots$genesBoxplot <- res
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+
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+ res
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1768
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})
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1758
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1770
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1759
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# for reading in the brushed/clicked points
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...
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...
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@@ -1933,47 +1922,38 @@ pcaExplorer <- function(dds = NULL,
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1933
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1922
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onlyfactors <- genedata[, match(input$color_by, colnames(genedata))]
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1934
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1923
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genedata$plotby <- interaction(onlyfactors)
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1935
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1924
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genedata$sampleID <- rownames(genedata)
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1936
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-
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1937
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- # input$plot_style chooses the style of plotting
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1925
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+
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1938
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1926
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if (input$plot_style == "boxplot") {
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1939
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- res <- ggplot(genedata, aes_string(x = "plotby", y = "count", fill = "plotby")) +
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1940
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- geom_boxplot(outlier.shape = NA, alpha = 0.7) + theme_bw()
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1941
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- if (input$ylimZero) {
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1942
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))
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1943
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- } else {
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1944
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale")
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1945
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- }
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1946
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-
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1947
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- res <- res +
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1948
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- labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +
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1949
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- scale_x_discrete(name = "") +
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1950
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- geom_jitter(aes_string(x = "plotby", y = "count"), position = position_jitter(width = 0.1)) +
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1951
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- scale_fill_discrete(name = "Experimental\nconditions")
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1952
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- if (input$addsamplelabels) {
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1953
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- res <- res + geom_text(aes_string(label = "sampleID"), hjust = -.1, vjust = 0)
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1954
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- }
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1955
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- exportPlots$genefinder_countsplot <- res
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1956
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- res
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1927
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+ plot_style <- "boxplot"
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1957
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1928
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} else if (input$plot_style == "violin plot") {
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1958
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- res <- ggplot(genedata, aes_string(x = "plotby", y = "count", fill = "plotby")) +
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1959
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- geom_violin(aes_string(col = "plotby"), alpha = 0.6) + theme_bw()
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1960
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- if (input$ylimZero) {
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1961
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))
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1962
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- } else {
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1963
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- res <- res + scale_y_log10(name = "Normalized counts - log10 scale")
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1964
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- }
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1965
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-
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1966
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- res <- res +
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1967
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- labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +
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1968
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- scale_x_discrete(name = "") +
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1969
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- geom_jitter(aes_string(x = "plotby", y = "count"), alpha = 0.8, position = position_jitter(width = 0.1)) +
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1970
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- scale_fill_discrete(name = "Experimental\nconditions") + scale_color_discrete(guide = "none")
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1971
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- if (input$addsamplelabels) {
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1972
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- res <- res + geom_text(aes_string(label = "sampleID"), hjust = -.1, vjust = 0)
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1973
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- }
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1974
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- exportPlots$genefinder_countsplot <- res
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1975
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- res
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1929
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+ plot_style <- "violin"
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1930
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+ } else {
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1931
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+ plot_style <- "auto"
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1932
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+ }
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1933
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+
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1934
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+ res <- mosdef::gene_plot(de_container = values$mydds,
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1935
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+ gene = selectedGene,
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1936
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+ intgroup = input$color_by,
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1937
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+ annotation_obj = values$myannotation,
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1938
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+ normalized = TRUE,
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1939
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+ labels_display = input$addsamplelabels,
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1940
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+ plot_type = plot_style)
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1941
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+
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1942
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+ if (input$ylimZero) {
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1943
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+ res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))
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1944
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+ } else {
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1945
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+ res <- res + scale_y_log10(name = "Normalized counts - log10 scale")
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1976
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1946
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}
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1947
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+
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1948
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+ res <- res +
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1949
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+ labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +
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1950
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+ scale_x_discrete(name = "") +
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1951
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+ scale_fill_discrete(name = "Experimental\nconditions")
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1952
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+
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1953
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+ exportPlots$genefinder_countsplot <- res
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1954
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+
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1955
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+ res
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1956
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+
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1977
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1957
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})
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1978
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1958
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1979
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1959
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output$genefinder_table <- DT::renderDataTable({
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