[BioC] trouble in loading heatmap.2

[James W. MacDonald]

Hi Wei,

First, gplots is a CRAN package so you should be asking about this on 
R-help, not Bioc-help.

However, you might try re-installing, as the function is definitely there:

 > library(gplots)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

 > args(heatmap.2)
function (x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
distfun = dist, hclustfun = hclust, dendrogram = c("both",
"row", "column", "none"), symm = FALSE, scale = c("none",
"row", "column"), na.rm = TRUE, revC = identical(Colv,
"Rowv"), add.expr, breaks, symbreaks = min(x < 0, na.rm = TRUE) ||
scale != "none", col = "heat.colors", colsep, rowsep,
sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote, notecex = 1,
notecol = "cyan", na.color = par("bg"), trace = c("column",
"row", "both", "none"), tracecol = "cyan", hline = median(breaks),
vline = median(breaks), linecol = tracecol, margins = c(5,
5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL,
srtRow = NULL, srtCol = NULL, adjRow = c(0, NA), adjCol = c(NA,
0), offsetRow = 0.5, offsetCol = 0.5, key = TRUE, keysize = 1.5,
density.info = c("histogram", "density", "none"), denscol = tracecol,
symkey = min(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
main = NULL, xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL,
lwid = NULL, ...)
NULL
 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] gplots_2.12.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 gtools_3.3.0
[5] KernSmooth_2.23-10

Best,

Jim



On 2/20/2014 3:42 PM, Wei Xu wrote:
> Hi,
>
> This is probably not common but after I update R tp 3.0.2, the heatmap.2
> cannot be found in gplots. I'm sure that I loaded the gplots already but
> whenever I tried heatmap.2, I was told that this function cannot be found.
> It didn't seem to be reported in this list so I guess it's just my problem.
> Thanks.
>
> Wei
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099