From 2880405a518bbbca8b3b9220b14af0f6d26c8d0b Mon Sep 17 00:00:00 2001
From: Julie Laffy <julie.laffy@weizmann.ac.il>
Date: Tue, 26 Sep 2023 16:16:30 +0300
Subject: [PATCH] unlogtpm and GGsave

---
 R/GGsave.R               | 12 ++++++++++--
 R/unlogtpm.R             |  4 ++--
 man/grouped_rowcenter.Rd |  2 +-
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/R/GGsave.R b/R/GGsave.R
index 8b801d2..6622203 100644
--- a/R/GGsave.R
+++ b/R/GGsave.R
@@ -1,5 +1,13 @@
-GGsave = function(filename, plot = last_plot()) {
+GGsave = function(filename, 
+		  plot=last_plot(), 
+		  width=dev.size()[1],
+		  height=dev.size()[2]) {
+
     device = 'png'
     if (str_detect(filename, "pdf")) device = 'pdf'
-    ggsave(filename = filename, plot = plot, width = dev.size()[1], height = dev.size()[2], device = device)
+    ggsave(filename=filename,
+	   plot=plot,
+	   width=width,
+	   height=height,
+	   device=device)
 }
diff --git a/R/unlogtpm.R b/R/unlogtpm.R
index 1c50e34..4bfc519 100644
--- a/R/unlogtpm.R
+++ b/R/unlogtpm.R
@@ -12,7 +12,7 @@ unlogtpm = function(m, bulk = F) {
     if (has_dim(m)) m = as.matrix(m)
     if (bulk) x = 1
     else x = 10
-    (2^m) * x - 1 
-    #x * (2^(m) - 1)
+    #(2^m) * x - 1 
+    (2^(m) - 1) * x
 }
 
diff --git a/man/grouped_rowcenter.Rd b/man/grouped_rowcenter.Rd
index 288bcbb..23a0736 100644
--- a/man/grouped_rowcenter.Rd
+++ b/man/grouped_rowcenter.Rd
@@ -17,5 +17,5 @@ grouped_rowcenter(m, groups = split_by_sample_names(colnames(m)), by = "mean")
 A row-centered matrix, centered within groups and with the order of cells within groups retained. The matrix has the same number of rows as <m> and as many columns as there are cell ids in groups.
 }
 \description{
-Center matrix rows by subsets of columns
+
 }