[R] problem with heatmap.2 in package gplots generating non-finite breaks
Mark Kimpel
mwkimpel at gmail.com
Tue Jul 21 16:53:17 CEST 2009
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<mwkimpel at 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
> ******************************************************************
>
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