diff --git a/R/plot_functions_explore.R b/R/plot_functions_explore.R index 1d51e36..bcb445d 100644 --- a/R/plot_functions_explore.R +++ b/R/plot_functions_explore.R @@ -39,7 +39,7 @@ #' dep <- add_rejections(diff, alpha = 0.05, lfc = 1) #' #' plot_pca(dep) -#' plot_pca(dep, indicate = "") +#' plot_pca(dep, indicate = "condition") #' @export plot_pca <- function(dep, x = 1, y = 2, indicate = c("condition", "replicate"), label = FALSE, n = 500, point_size = 6, label_size = 3) { @@ -173,6 +173,8 @@ plot_pca <- function(dep, x = 1, y = 2, indicate = c("condition", "replicate"), #' Sets the color panel (from \code{\link[RColorBrewer]{brewer.pal}}). #' @param pal_rev Logical(1), #' Whether or not to invert the color palette. +#' @param font_size Integer(1), +#' Sets the size of the labels. #' @param ... Additional arguments for Heatmap function as depicted in #' \code{\link[ComplexHeatmap]{Heatmap}} #' @return A heatmap plot (generated by \code{\link[ComplexHeatmap]{Heatmap}}) @@ -193,7 +195,7 @@ plot_pca <- function(dep, x = 1, y = 2, indicate = c("condition", "replicate"), #' diff <- test_diff(imputed, 'Ctrl', 'control') #' dep <- add_rejections(diff, alpha = 0.05, lfc = 1) #' -#' plot_corr(dep) +#' plot_cor(dep) #' @export plot_cor <- function(dep, significant = TRUE, lower = -1, upper = 1, pal = "PRGn", pal_rev = FALSE, font_size = 12, ...) { diff --git a/man/plot_cor.Rd b/man/plot_cor.Rd index 9baedb4..99910f1 100644 --- a/man/plot_cor.Rd +++ b/man/plot_cor.Rd @@ -27,6 +27,9 @@ Sets the color panel (from \code{\link[RColorBrewer]{brewer.pal}}).} \item{pal_rev}{Logical(1), Whether or not to invert the color palette.} +\item{font_size}{Integer(1), +Sets the size of the labels.} + \item{...}{Additional arguments for Heatmap function as depicted in \code{\link[ComplexHeatmap]{Heatmap}}} } @@ -53,5 +56,5 @@ imputed <- impute(norm, fun = 'MinProb', q = 0.01) diff <- test_diff(imputed, 'Ctrl', 'control') dep <- add_rejections(diff, alpha = 0.05, lfc = 1) -plot_corr(dep) +plot_cor(dep) } diff --git a/man/plot_pca.Rd b/man/plot_pca.Rd index 047b29c..74a24d7 100644 --- a/man/plot_pca.Rd +++ b/man/plot_pca.Rd @@ -58,5 +58,5 @@ diff <- test_diff(imputed, 'Ctrl', 'control') dep <- add_rejections(diff, alpha = 0.05, lfc = 1) plot_pca(dep) -plot_pca(dep, indicate = "") +plot_pca(dep, indicate = "condition") }