Never mind, the problem seems to be that I have ignored the warning "Using scale="row" or scale="column" when breaks arespecified can produce unpredictable results.Please consider using only one or the other."
I just stop specifying the breaks and it works fine. Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Tue, Jul 21, 2009 at 10:28 AM, Mark Kimpel<mwkim...@gmail.com> wrote: > I have written a wrapper for heatmap.2 called > heatmap.w.row.and.col.clust which auto-generates breaks using > breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, > digits = 2) #(stddev in this case = 2.5) > > This has always worked well in the past but now I am getting an error > that non-finite breaks are being generated. Drilling down, it seems > that my wrapper is generating finite breaks but for some reason > heatmap.2 is putting a NaN into the first and last positions in the > vector. > > Is it obvious using the breaks my wrapper has generated why this > should be so? My sessionInfo() follows. > > Thanks, Mark > > Browse[1]> c > > Enter a frame number, or 0 to exit > > 1: heatmap.w.row.and.col.clust(iqa.corp.sparse.rem) > 2: heatmap.func.R#29: heatmap.2(as.matrix(dataframe), col = color.palette, bre > 3: image(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, xaxt = "n", y > 4: image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, xaxt > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "breaks" "col.labels" "color.palette" > [4] "dataframe" "dendrogram.options" "remove.mean" > [7] "row.labels" "stddev" > Browse[1]> breaks > [1] -2.50 -2.45 -2.40 -2.35 -2.30 -2.25 -2.20 -2.15 -2.10 -2.05 -2.00 -1.95 > [13] -1.90 -1.85 -1.80 -1.75 -1.70 -1.65 -1.60 -1.55 -1.50 -1.45 -1.40 -1.35 > [25] -1.30 -1.25 -1.20 -1.15 -1.10 -1.05 -1.00 -0.95 -0.90 -0.85 -0.80 -0.75 > [37] -0.70 -0.65 -0.60 -0.55 -0.50 -0.45 -0.40 -0.35 -0.30 -0.25 -0.20 -0.15 > [49] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 > [61] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.05 > [73] 1.10 1.15 1.20 1.25 1.30 1.35 1.40 1.45 1.50 1.55 1.60 1.65 > [85] 1.70 1.75 1.80 1.85 1.90 1.95 2.00 2.05 2.10 2.15 2.20 2.25 > [97] 2.30 2.35 2.40 2.45 2.50 > Browse[1]> is.finite(breaks) > [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE > [91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > Browse[1]> c > > Enter a frame number, or 0 to exit > > 1: heatmap.w.row.and.col.clust(iqa.corp.sparse.rem) > 2: heatmap.func.R#29: heatmap.2(as.matrix(dataframe), col = color.palette, bre > 3: image(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, xaxt = "n", y > 4: image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, xaxt > > Selection: 2 > Called from: eval(expr, envir, enclos) > Browse[1]> heatmap.func.R > Error during wrapup: object 'heatmap.func.R' not found > Browse[1]> ls() > [1] "add.expr" "breaks" "cellnote" "cexCol" > [5] "cexRow" "col" "colInd" "colsep" > [9] "ColSideColors" "Colv" "ddc" "ddr" > [13] "dendrogram" "densadj" "denscol" "density.info" > [17] "di" "distfun" "hcc" "hclustfun" > [21] "hcr" "hline" "iy" "key" > [25] "keysize" "labCol" "labRow" "lhei" > [29] "linecol" "lmat" "lwid" "main" > [33] "margins" "max.breaks" "max.raw" "max.scale" > [37] "min.breaks" "min.raw" "min.scale" "mmat" > [41] "na.color" "na.rm" "nbr" "nc" > [45] "ncol" "notecex" "notecol" "nr" > [49] "op" "retval" "revC" "rm" > [53] "rowInd" "rowsep" "RowSideColors" "Rowv" > [57] "scale" "scale01" "sepcolor" "sepwidth" > [61] "sx" "symbreaks" "symkey" "symm" > [65] "tmpbreaks" "trace" "tracecol" "vline" > [69] "x" "xlab" "x.scaled" "x.unscaled" > [73] "ylab" "z" > Browse[1]> tmpbreaks > [1] NaN -2.45 -2.40 -2.35 -2.30 -2.25 -2.20 -2.15 -2.10 -2.05 -2.00 -1.95 > [13] -1.90 -1.85 -1.80 -1.75 -1.70 -1.65 -1.60 -1.55 -1.50 -1.45 -1.40 -1.35 > [25] -1.30 -1.25 -1.20 -1.15 -1.10 -1.05 -1.00 -0.95 -0.90 -0.85 -0.80 -0.75 > [37] -0.70 -0.65 -0.60 -0.55 -0.50 -0.45 -0.40 -0.35 -0.30 -0.25 -0.20 -0.15 > [49] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 > [61] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.05 > [73] 1.10 1.15 1.20 1.25 1.30 1.35 1.40 1.45 1.50 1.55 1.60 1.65 > [85] 1.70 1.75 1.80 1.85 1.90 1.95 2.00 2.05 2.10 2.15 2.20 2.25 > [97] 2.30 2.35 2.40 2.45 NaN > Browse[1]> sessionInfo() > R version 2.10.0 Under development (unstable) (2009-05-31 r48697) > x86_64-unknown-linux-gnu > > 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=C 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] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] gplots_2.7.1 caTools_1.9 bitops_1.0-4.1 gmodels_2.15.0 gtools_2.6.1 > [6] gdata_2.4.2 tm_0.4 > > loaded via a namespace (and not attached): > [1] MASS_7.3-0 rJava_0.6-3 RWeka_0.3-20 slam_0.1-1 Snowball_0.0-6 > [6] tcltk_2.10.0 tools_2.10.0 > Browse[1]> > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > > "The real problem is not whether machines think but whether men do." > -- B. F. Skinner > ****************************************************************** > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
