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@@ -63,7 +63,7 @@ gosummaries_base = function(x){ |
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comp$Percentage = sprintf("Up: %d\nDown: %d", length(x[[i]][[2]]), length(x[[i]][[1]]))
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}
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- res[[as.character(components[i])]] = comp
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+ res[[i]] = comp
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}
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class(res) = "gosummaries"
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@@ -287,8 +287,6 @@ annotate.gosummaries = function(gosummaries, organism, components = 1:length(gos |
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if(!is.gosummaries(gosummaries)) stop("Function requires a gosummaries type of object")
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- components = as.character(components)
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-
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#Compile gene lists
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gl = NULL
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for(i in seq_along(components)){
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@@ -312,9 +310,9 @@ annotate.gosummaries = function(gosummaries, organism, components = 1:length(gos |
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k = 1
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for(i in seq_along(components)){
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- for(j in seq_along(gosummaries[[components[i]]]$GPR)){
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+ for(j in seq_along(gosummaries[[i]]$GPR)){
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lname = paste("gpr", j, sep = "")
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- gosummaries[[components[i]]]$GPR[[lname]] = gpr[gpr$query.number == k, -1]
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+ gosummaries[[i]]$GPR[[lname]] = gpr[gpr$query.number == k, -1]
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k = k + 1
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}
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}
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@@ -856,8 +854,6 @@ panel_crossbar = function(data, fontsize = 10, par){ |
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#' of a gosummaries object. The legend and the actual plots for the panels are extracted
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#' later from the figure produced by this function.
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#' @author Raivo Kolde <rkolde@@gmail.com>
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-#' @examples
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-#' # Example1
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#'
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#' @rdname panel_boxplot
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#' @export
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@@ -1009,8 +1005,7 @@ customize = function(p, par){ |
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#' differential expression it draws the boxplot of expression values.
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#'
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#' @param x a gosummaries object
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-#' @param components names of the gosummaries components to draw. The names are usually
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-#' numbers 1:n in character format.
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+#' @param components names of the gosummaries components to draw.
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#' @param classes name of the variable from annotation data.frame that defines the colors in the plot
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#' @param panel_plot plotting function for panel
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#' @param panel_customize customization function for the panel plot, menat for making
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@@ -1043,7 +1038,7 @@ customize = function(p, par){ |
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#' plot(gs_limma, panel_height = 0, fontsize = 8)
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#'
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#' # Selecting only certain components
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-#' plot(gs_limma, components = as.character(c(1, 3)), fontsize = 8)
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+#' plot(gs_limma, components = c(1, 3), fontsize = 8)
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#'
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#' # Cutting the longer terms shorter (see the effect on the right wordcloud on first component)
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#' plot(gs_limma, term_length = 20, fontsize = 8)
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@@ -1054,24 +1049,24 @@ customize = function(p, par){ |
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#' # Adjust panel plot type (see panel_boxplot help for options)
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#' data(gs_kmeans)
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#'
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-#' plot(gs_kmeans, panel_plot = panel_violin, classes = "Tissue", components = c("1", "2"), fontsize = 8)
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-#' plot(gs_kmeans, panel_plot = panel_violin_box, classes = "Tissue", components = c("1", "2"), fontsize = 8)
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+#' plot(gs_kmeans, panel_plot = panel_violin, classes = "Tissue", components = 1:2, fontsize = 8)
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+#' plot(gs_kmeans, panel_plot = panel_violin_box, classes = "Tissue", components = 1:2, fontsize = 8)
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#'
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#' # Adjust colorscheme for plot (see customize help for more information)
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#' cust = function(p, par){
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#' p = p + scale_fill_brewer(par$classes, type = "qual", palette = 2)
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#' return(p)
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#' }
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-#' plot(gs_kmeans, panel_plot = panel_violin, panel_customize = cust, classes = "Tissue", components = c("1", "2"), fontsize = 8)
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+#' plot(gs_kmeans, panel_plot = panel_violin, panel_customize = cust, classes = "Tissue", components = 1:2, fontsize = 8)
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#'
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#' @method plot gosummaries
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#'
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#' @export
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-plot.gosummaries = function(x, components = names(x)[1:min(10, length(x))], classes = NA, panel_plot = NULL, panel_customize = NULL, panel_par = list(), panel_height = 5, panel_width = 30, fontsize = 10, term_length = 35, wordcloud_colors = c("grey70", "grey10"), filename = NA, ...){
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+plot.gosummaries = function(x, components = 1:min(10, length(x)), classes = NA, panel_plot = NULL, panel_customize = NULL, panel_par = list(), panel_height = 5, panel_width = 30, fontsize = 10, term_length = 35, wordcloud_colors = c("grey70", "grey10"), filename = NA, ...){
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# Check input
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if(!is.gosummaries(x)) stop("Function requires an object of gosummaries type")
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- if(any(!(as.character(components) %in% names(x)))) stop("Selected components are not present in data")
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+ if(any(!(components %in% 1:length(x)))) stop("Selected components are not present in data")
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# Add classes to panel_par
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if(!is.na(classes)){
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@@ -1084,7 +1079,7 @@ plot.gosummaries = function(x, components = names(x)[1:min(10, length(x))], clas |
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}
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# Take out components of interest
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- x = x[as.character(components)]
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+ x = x[components]
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if(length(x) < 1) stop("No components selected")
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# Add wordcloud colors and adjust the string length
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@@ -1242,8 +1237,8 @@ gosummaries.prcomp = function(x, annotation = NULL, components = 1:6, n_genes = |
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#'
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#' # Create gosummaries object
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#' gs_kmeans = gosummaries(kmr, exp = exp2, annotation = tissue_example$annot)
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-#' plot(gs_kmeans, panel_height = 0, components = c("1", "2", "3"), fontsize = 8)
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-#' plot(gs_kmeans, classes = "Tissue", components = c("1", "2", "3"), fontsize = 8)
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+#' plot(gs_kmeans, panel_height = 0, components = 1:3, fontsize = 8)
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+#' plot(gs_kmeans, classes = "Tissue", components = 1:3, fontsize = 8)
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#'
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#' @method gosummaries kmeans
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#' @S3method gosummaries kmeans
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raivokolde
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