changed (multi|ez)heat height & width defaults

Author: jdreyf

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ezlimmaplot
 Title: Bioinformatics plots using limma and ggplot2, some from output of ezlimma
-Version: 0.0.4.9000
+Version: 0.0.4.9001
 Authors@R: c(person("Jonathan", "Dreyfuss", role = c("aut", "cre"), email = "jdreyf@bu.edu"),
              person("Hui", "Pan", role = "aut"),
 			 person("Grace", "Daher", role="ctb"))

R/ezheat.R

@@ -54,7 +54,7 @@ ezheat <- function(object, pheno.df=NULL, labrows=rownames(object), labcols=coln
                    color.v=NULL, unique.rows=FALSE, only.labrows=FALSE, ntop=NULL, stat.tab = NULL,
                    cutoff = 0.05, reorder_rows=FALSE, reorder_cols=FALSE, gaps_row = NULL, gaps_col = NULL,
                    annotation_row = NA, annotation_colors = NA, angle_col=c("270", "0", "45", "90", "315"),
-                   fontsize_row=10, fontsize_col=10, na.lab=c("---", ""), plot=TRUE, width=NA, height=NA, verbose=FALSE){
+                   fontsize_row=10, fontsize_col=10, na.lab=c("---", ""), plot=TRUE, width=7, height=7, verbose=FALSE){
   angle_col <- match.arg(angle_col)
   if (!is.matrix(object)) object <- data.matrix(object)
   stopifnot(sum(is.na(object)) == 0, sc %in% c("ctr", "z", "none"), is.na(clip) | (length(clip)==1 && clip > 0),

R/multi_heat.R

@@ -16,7 +16,7 @@ multi_heat <- function(tab, object, pheno.df=NULL, labrows=rownames(object), lab
                        main="Log2 Expression", name="heats", sc="ctr", clip=NA, color.v=NULL,
                        unique.rows=FALSE, only.labrows=FALSE, ntop=50, stat.tab = NULL,
                        cutoff = 0.05, reorder_rows=TRUE, reorder_cols=FALSE, fontsize_row=10, fontsize_col=10,
-                       na.lab=c("---", ""), plot=TRUE, width=NA, height=NA, verbose=FALSE){
+                       na.lab=c("---", ""), plot=TRUE, width=7, height=7, verbose=FALSE){
   if (length(labrows)==1) labrows <- rep(x=labrows, nrow(object))
   stopifnot(length(labrows)==nrow(object), names(labrows)==rownames(object))
   if (any(labrows != rownames(object))) stopifnot(!is.null(names(labrows)))
@@ -43,11 +43,11 @@ multi_heat <- function(tab, object, pheno.df=NULL, labrows=rownames(object), lab
                                color.v=color.v, unique.rows=unique.rows, only.labrows=only.labrows, ntop=ntop,
                                stat.tab = stat.tab, cutoff = cutoff, labcols=labcols, reorder_rows=reorder_rows,
                                reorder_cols=reorder_cols, fontsize_row=fontsize_row, fontsize_col=fontsize_col,
-                               na.lab=na.lab, plot=FALSE, width=width, height=height, verbose=verbose, name=NA)
+                               na.lab=na.lab, plot=FALSE, verbose=verbose, name=NA)
   }
   if (plot){
     if (!is.na(name)) {
-      grDevices::pdf(paste0(name, ".pdf"))
+      grDevices::pdf(paste0(name, ".pdf"), width = width, height = height)
       on.exit(grDevices::dev.off())
     }
     for (contr in contr.names){