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.
