trouble in loading heatmap.2
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Wei Xu ▴ 30
@wei-xu-4939
Last seen 9.6 years ago
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 -- Wei Xu, Ph.D. Wound Healing and Regenerative Medicine Laboratory Department of Surgery / Plastic Surgery Division Northwestern University, Feinberg School of Medicine 303 East Chicago Ave, Tarry 4-720 Chicago, IL 60611 Phone: (312) 908 0566 Fax: (312) 908 4013 [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 1 minute ago
United States
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
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Thanks, James. The problem is fixed. Some of the packages in gplots are missing. Manually installation in needed in my system... Wei On Thu, Feb 20, 2014 at 2:49 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > 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 > > -- Wei Xu, Ph.D. Wound Healing and Regenerative Medicine Laboratory Department of Surgery / Plastic Surgery Division Northwestern University, Feinberg School of Medicine 303 East Chicago Ave, Tarry 4-720 Chicago, IL 60611 Phone: (312) 908 0566 Fax: (312) 908 4013 [[alternative HTML version deleted]]
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