[BioC] small bug in overview function of made4

[Jenny Drnevich]

Hi Aedin,

I noticed a change in the behavior of your overview function in the 
made4 package from BioC 2.4 to BioC 2.5. Before, when I only wanted 
to plot the hc dendrogram, it completely filled the plotting window. 
However, now no matter what combinations of hc, boxplot and hist, the 
window is always divided up into 3 sections. I looked at the code, 
and there seems to be one change that's causing the bug:

 >overview
function (dataset, labels = NULL, title = "", classvec = NULL,
     hc = TRUE, boxplot = TRUE, hist = TRUE, returnTree = FALSE)
{
     cols = NULL
     if (sum(boxplot, hist, hc) == 3)
         layout(matrix(c(1, 1, 2, 3), 2, 2, byrow = TRUE))
     if (sum(boxplot, hist, hc) == 2)
         layout(matrix(c(1, 1, 2, 2), 2, 2, byrow = TRUE))
     classvec = as.factor(classvec)

This last line is new, and changes the default NULL value into a 
factor, such that a few lines farther down in the code:

if (!is.null(classvec)) {
         cols = getcol(as.numeric(classvec))
         layout(matrix(c(1, 1, 2, 2, 3, 4), 3, 2, byrow = TRUE),
             heights = c(1.5, 0.1, 2))
     }

!is.null(classvec) is now TRUE, even if classvec was originally NULL.


And since I've e-mailed you, I'll say that I always thought it was 
weird that the main title for the hierarchical clustering dendrogram 
was "Histogram", not "Dendrogram":

plot(hc, hang = -1, labels = labels, main = paste("Histogram",
             title, sep = " "), sub = "", xlab = "")

Thanks!
Jenny

 > sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] grid      stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
  [1] limma_3.2.1          affyQCReport_1.24.0  lattice_0.17-26
  [4] xtable_1.5-5         simpleaffy_2.22.0    genefilter_1.28.0
  [7] made4_1.20.0         scatterplot3d_0.3-29 gplots_2.7.3
[10] caTools_1.10         bitops_1.0-4.1       gdata_2.6.1
[13] gtools_2.6.1         RColorBrewer_1.0-2   ade4_1.4-11
[16] affyPLM_1.22.0       preprocessCore_1.8.0 gcrma_2.18.0
[19] affycoretools_1.18.0 KEGG.db_2.3.5        GO.db_2.3.5
[22] RSQLite_0.7-3        DBI_0.2-4            AnnotationDbi_1.8.0
[25] affy_1.24.0          Biobase_2.6.0        RWinEdt_1.8-1

loaded via a namespace (and not attached):
  [1] affyio_1.14.0     annaffy_1.18.0    annotate_1.24.0   biomaRt_2.2.0
  [5] Biostrings_2.14.0 Category_2.12.0   GOstats_2.12.0    graph_1.24.0
  [9] GSEABase_1.8.0    IRanges_1.4.0     RBGL_1.20.0       RCurl_1.2-1
[13] splines_2.10.0    survival_2.35-7   tools_2.10.0      XML_2.6-0






Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu