From f20c0f87202bcd20e4fcb56543cf30e45fe620c0 Mon Sep 17 00:00:00 2001
From: vertesy <abel.vertesy@imba.oeaw.ac.at>
Date: Wed, 24 Jul 2024 16:41:30 +0200
Subject: [PATCH] bug in wplot_save_pheatmap The problem was in width and
 height calculation

---
 R/MarkdownReports.R        |  9 ++++++---
 man/wplot_save_pheatmap.Rd | 17 ++++++++++++-----
 2 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/R/MarkdownReports.R b/R/MarkdownReports.R
index c0a7f32..a0977f2 100644
--- a/R/MarkdownReports.R
+++ b/R/MarkdownReports.R
@@ -407,6 +407,7 @@ wplot_save_this <- function(plotname = ww.autoPlotName(),
 #' @description Save pheatmap object. Modified from:
 #' https://stackoverflow.com/questions/43051525/how-to-draw-pheatmap-plot-to-screen-and-also-save-to-file
 #' @param x The pheatmap object to save.
+#' @param data data matrix used to create the pheatmap object. Only used to define plot height and width.
 #' @param suffix Suffix to File name. Default: 'heatmap'.
 #' @param plotname Name of the plot. Default: substitute(x). File saved as .pdf, inside working
 #' directory.
@@ -429,11 +430,12 @@ wplot_save_this <- function(plotname = ww.autoPlotName(),
 #' ph.test <- pheatmap::pheatmap(test)
 #' wplot_save_pheatmap(ph.test)
 wplot_save_pheatmap <- function(x,
+                                data = NULL,
                                 suffix = "heatmap",
                                 plotname = as.character(substitute(x)),
                                 add = 1,
-                                width = max(length(x$tree_col$labels)+add, 4),
-                                height = max(length(x$tree_row$labels)-add, 4),
+                                width = max(if(is.null(data)) 7 else ncol(data) + add, 4),
+                                height = max(if(is.null(data)) 7 else nrow(data) - add, 4),
                                 pdf = TRUE,
                                 png = FALSE,
                                 png_res = 100, # NA
@@ -441,7 +443,8 @@ wplot_save_pheatmap <- function(x,
                                 mdlink = TRUE) {
   #
   stopifnot(inherits(x, "pheatmap"),
-            is.character(suffix), is.character(plotname), is.numeric(add), is.numeric(width), is.numeric(height),
+            is.character(suffix), is.character(plotname), nchar(plotname) < 200,
+            is.numeric(add), is.numeric(width), is.numeric(height),
             is.logical(pdf), is.logical(png), is.numeric(png_res), is.numeric(png_dim_factor), is.logical(mdlink)
   )
 
diff --git a/man/wplot_save_pheatmap.Rd b/man/wplot_save_pheatmap.Rd
index 492e3ca..972281e 100644
--- a/man/wplot_save_pheatmap.Rd
+++ b/man/wplot_save_pheatmap.Rd
@@ -6,10 +6,12 @@
 \usage{
 wplot_save_pheatmap(
   x,
+  data = NULL,
   suffix = "heatmap",
-  plotname = substitute(x),
-  width = nrow(x) + 4,
-  height = ncols(x) + 4,
+  plotname = as.character(substitute(x)),
+  add = 1,
+  width = max(if (is.null(data)) 7 else ncol(data) + add, 4),
+  height = max(if (is.null(data)) 7 else nrow(data) - add, 4),
   pdf = TRUE,
   png = FALSE,
   png_res = 100,
@@ -20,8 +22,15 @@ wplot_save_pheatmap(
 \arguments{
 \item{x}{The pheatmap object to save.}
 
+\item{data}{data matrix used to create the pheatmap object. Only used to define plot height and width.}
+
 \item{suffix}{Suffix to File name. Default: 'heatmap'.}
 
+\item{plotname}{Name of the plot. Default: substitute(x). File saved as .pdf, inside working
+directory.}
+
+\item{add}{Constant to add to width and height. Default: 2.}
+
 \item{width}{width of the plot in inches.}
 
 \item{height}{height of the plot in inches.}
@@ -36,8 +45,6 @@ wplot_save_pheatmap(
 
 \item{mdlink}{Insert a .pdf and a .png image link in the markdown report, set by
 "path_of_report".}
-
-\item{filename}{File name (saved as .pdf, inside working directory).}
 }
 \description{
 Save pheatmap object. Modified from: