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R version 3.6.2 Patched (2020-01-11 r77654) -- "Dark and Stormy Night"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> suppressMessages(library(gplots))
> data(mtcars)
> x <- as.matrix(mtcars)
> rc <- rainbow(nrow(x), start=0, end=.3)
> cc <- rainbow(ncol(x), start=0, end=.3)
>
> heatmap.2(x) ## default - dendrogram plotted and reordering done.
> heatmap.2(x, dendrogram="none") ## no dendrogram plotted, but reordering done.
> heatmap.2(x, dendrogram="row") ## row dendrogram plotted and row reordering done.
> heatmap.2(x, dendrogram="col") ## col dendrogram plotted and col reordering done.
>
> heatmap.2(x, keysize=2) ## default - dendrogram plotted and reordering done.
>
>
> heatmap.2(x, Colv=FALSE)
Warning message:
In heatmap.2(x, Colv = FALSE) :
Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting column dendogram.
> heatmap.2(x, Colv=NULL)
Warning message:
In heatmap.2(x, Colv = NULL) :
Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting column dendogram.
>
> heatmap.2(x, Rowv=FALSE)
Warning message:
In heatmap.2(x, Rowv = FALSE) :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
> heatmap.2(x, Rowv=NULL)
Warning message:
In heatmap.2(x, Rowv = NULL) :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
>
> heatmap.2(x, Rowv=FALSE, dendrogram="both") ## generate warning!
Warning message:
In heatmap.2(x, Rowv = FALSE, dendrogram = "both") :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
> heatmap.2(x, Rowv=NULL, dendrogram="both") ## generate warning!
Warning message:
In heatmap.2(x, Rowv = NULL, dendrogram = "both") :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
> heatmap.2(x, Colv=FALSE, dendrogram="both") ## generate warning!
Warning message:
In heatmap.2(x, Colv = FALSE, dendrogram = "both") :
Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting column dendogram.
>
>
>
> heatmap.2(x,dendrogram="both", Rowv=FALSE) ## row and col reordering done, but only col dendrogram plotted
Warning message:
In heatmap.2(x, dendrogram = "both", Rowv = FALSE) :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
> heatmap.2(x,dendrogram="row", Rowv=FALSE)
Warning message:
In heatmap.2(x, dendrogram = "row", Rowv = FALSE) :
Discrepancy: Rowv is FALSE, while dendrogram is `row'. Omitting row dendogram.
>
>
> heatmap.2(x,dendrogram="col", Rowv=FALSE)
> heatmap.2(x,dendrogram="none", Rowv=FALSE)
>
>
> heatmap.2(x,dendrogram="both", Colv=FALSE) ## row and col reordering done, but only row dendrogram plotted
Warning message:
In heatmap.2(x, dendrogram = "both", Colv = FALSE) :
Discrepancy: Colv is FALSE, while dendrogram is `both'. Omitting column dendogram.
> heatmap.2(x,dendrogram="row", Colv=FALSE)
> heatmap.2(x,dendrogram="col", Colv=FALSE)
Warning message:
In heatmap.2(x, dendrogram = "col", Colv = FALSE) :
Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
> heatmap.2(x,dendrogram="none", Colv=FALSE)
>
> ## above statement is same as heatmap.2(x,Colv=FALSE)
> heatmap.2(x,dendrogram="col", Colv=FALSE) ## col reordering done, but no dendrogram plotted
Warning message:
In heatmap.2(x, dendrogram = "col", Colv = FALSE) :
Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
>
>
> hv <- heatmap.2(x, col=cm.colors(256), scale="column",
+ RowSideColors=rc, ColSideColors=cc, margin=c(5, 10),
+ xlab="specification variables", ylab= "Car Models",
+ main="heatmap(<Mtcars data>, \n ..., scale=\"column\")",
+ tracecol="green", density="density")
>
> ## IGNORE_RDIFF_BEGIN
> str(hv) # the two re-ordering index vectors
List of 13
$ rowInd : int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
$ colInd : int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
$ call : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green", margins = c(5, 10), ColSideColo| __truncated__ ...
$ colMeans : Named num [1:11] 6.188 0.406 0.438 2.812 3.217 ...
..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
$ colSDs : Named num [1:11] 1.786 0.499 0.504 1.615 0.978 ...
..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
$ carpet : num [1:11, 1:32] 1.015 1.19 -0.868 3.212 0.361 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:11] "cyl" "am" "vs" "carb" ...
.. ..$ : chr [1:32] "Maserati Bora" "Chrysler Imperial" "Lincoln Continental" "Cadillac Fleetwood" ...
$ rowDendrogram: ..--[dendrogram w/ 2 branches and 32 members at h = 425, midpoint = 8.58, value = 1267]
.. |--[dendrogram w/ 2 branches and 9 members at h = 215, midpoint = 1.84, value = 552]
.. | |--leaf "Maserati Bora" ( value.Maserati Bora = 63.2 )
.. | `--[dendrogram w/ 2 branches and 8 members at h = 135, midpoint = 2.69, value = 489]
.. | |--[dendrogram w/ 2 branches and 3 members at h = 40.8, midpoint = 0.75, value = 198]
.. | | |--leaf "Chrysler Imperial" ( value.Chrysler Imperial = 66 )
.. | | `--[dendrogram w/ 2 branches and 2 members at h = 15.6, midpoint = 0.5, value = 132]
.. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66.1 )
.. | | `--leaf "Cadillac Fleetwood" ( value.Cadillac Fleetwood = 66.2 )
.. | `--[dendrogram w/ 2 branches and 5 members at h = 102, midpoint = 1.62, value = 290]
.. | |--[dendrogram w/ 2 branches and 2 members at h = 40, midpoint = 0.5, value = 111]
.. | | |--leaf "Hornet Sportabout" ( value.Hornet Sportabout = 53.7 )
.. | | `--leaf "Pontiac Firebird" ( value.Pontiac Firebird = 57.4 )
.. | `--[dendrogram w/ 2 branches and 3 members at h = 21.3, midpoint = 0.75, value = 179]
.. | |--leaf "Ford Pantera L" ( value.Ford Pantera L = 61 )
.. | `--[dendrogram w/ 2 branches and 2 members at h = 10.1, midpoint = 0.5, value = 118]
.. | |--leaf "Camaro Z28" ( value.Camaro Z28 = 58.8 )
.. | `--leaf "Duster 360" ( value.Duster 360 = 59.7 )
.. `--[dendrogram w/ 2 branches and 23 members at h = 262, midpoint = 6.33, value = 716]
.. |--[dendrogram w/ 2 branches and 7 members at h = 103, midpoint = 2.06, value = 306]
.. | |--[dendrogram w/ 2 branches and 2 members at h = 33.6, midpoint = 0.5, value = 73.8]
.. | | |--leaf "Valiant" ( value.Valiant = 35 )
.. | | `--leaf "Hornet 4 Drive" ( value.Hornet 4 Drive = 38.7 )
.. | `--[dendrogram w/ 2 branches and 5 members at h = 51.8, midpoint = 1.62, value = 233]
.. | |--[dendrogram w/ 2 branches and 2 members at h = 14, midpoint = 0.5, value = 93.2]
.. | | |--leaf "AMC Javelin" ( value.AMC Javelin = 46 )
.. | | `--leaf "Dodge Challenger" ( value.Dodge Challenger = 47.2 )
.. | `--[dendrogram w/ 2 branches and 3 members at h = 2.14, midpoint = 0.75, value = 139]
.. | |--leaf "Merc 450SLC" ( value.Merc 450SLC = 46.4 )
.. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 92.9]
.. | |--leaf "Merc 450SE" ( value.Merc 450SE = 46.4 )
.. | `--leaf "Merc 450SL" ( value.Merc 450SL = 46.5 )
.. `--[dendrogram w/ 2 branches and 16 members at h = 142, midpoint = 3.59, value = 409]
.. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 74.9]
.. | |--leaf "Honda Civic" ( value.Honda Civic = 17.7 )
.. | `--[dendrogram w/ 2 branches and 3 members at h = 10.4, midpoint = 0.75, value = 57.2]
.. | |--leaf "Toyota Corolla" ( value.Toyota Corolla = 18.8 )
.. | `--[dendrogram w/ 2 branches and 2 members at h = 5.15, midpoint = 0.5, value = 38.4]
.. | |--leaf "Fiat X1-9" ( value.Fiat X1-9 = 18.9 )
.. | `--leaf "Fiat 128" ( value.Fiat 128 = 19.4 )
.. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.3, value = 334]
.. |--leaf "Ferrari Dino" ( value.Ferrari Dino = 34.5 )
.. `--[dendrogram w/ 2 branches and 11 members at h = 74.4, midpoint = 3.61, value = 300]
.. |--[dendrogram w/ 2 branches and 5 members at h = 64.9, midpoint = 1.25, value = 148]
.. | |--leaf "Merc 240D" ( value.Merc 240D = 24.6 )
.. | `--[dendrogram w/ 2 branches and 4 members at h = 15.7, midpoint = 1.5, value = 124]
.. | |--[dendrogram w/ 2 branches and 2 members at h = 0.615, midpoint = 0.5, value = 59.9]
.. | | |--leaf "Mazda RX4" ( value.Mazda RX4 = 29.9 )
.. | | `--leaf "Mazda RX4 Wag" ( value.Mazda RX4 Wag = 30 )
.. | `--[dendrogram w/ 2 branches and 2 members at h = 1.52, midpoint = 0.5, value = 63.6]
.. | |--leaf "Merc 280C" ( value.Merc 280C = 31.8 )
.. | `--leaf "Merc 280" ( value.Merc 280 = 31.9 )
.. `--[dendrogram w/ 2 branches and 6 members at h = 50.1, midpoint = 0.969, value = 152]
.. |--leaf "Lotus Europa" ( value.Lotus Europa = 24.9 )
.. `--[dendrogram w/ 2 branches and 5 members at h = 33.2, midpoint = 0.938, value = 127]
.. |--leaf "Merc 230" ( value.Merc 230 = 27.2 )
.. `--[dendrogram w/ 2 branches and 4 members at h = 20.7, midpoint = 0.875, value = 99.5]
.. |--leaf "Volvo 142E" ( value.Volvo 142E = 26.3 )
.. `--[dendrogram w/ 2 branches and 3 members at h = 13.1, midpoint = 0.75, value = 73.3]
.. |--leaf "Datsun 710" ( value.Datsun 710 = 23.6 )
.. `--[dendrogram w/ 2 branches and 2 members at h = 8.65, midpoint = 0.5, value = 49.7]
.. |--leaf "Porsche 914-2" ( value.Porsche 914-2 = 24.8 )
.. `--leaf "Toyota Corona" ( value.Toyota Corona = 24.9 )
$ colDendrogram: ..--[dendrogram w/ 2 branches and 11 members at h = 1475, midpoint = 7, value = 436]
.. |--[dendrogram w/ 2 branches and 9 members at h = 116, midpoint = 4.5, value = 58.3]
.. | |--[dendrogram w/ 2 branches and 7 members at h = 34.8, midpoint = 1.5, value = 20.3]
.. | | |--leaf "cyl" ( value.cyl = 6.19 )
.. | | `--[dendrogram w/ 2 branches and 6 members at h = 18.9, midpoint = 2, value = 14.2]
.. | | |--[dendrogram w/ 2 branches and 2 members at h = 3.61, midpoint = 0.5, value = 0.844]
.. | | | |--leaf "am" ( value.am = 0.406 )
.. | | | `--leaf "vs" ( value.vs = 0.438 )
.. | | `--[dendrogram w/ 2 branches and 4 members at h = 10.7, midpoint = 1.5, value = 13.3]
.. | | |--[dendrogram w/ 2 branches and 2 members at h = 8.6, midpoint = 0.5, value = 6.03]
.. | | | |--leaf "carb" ( value.carb = 2.81 )
.. | | | `--leaf "wt" ( value.wt = 3.22 )
.. | | `--[dendrogram w/ 2 branches and 2 members at h = 2.98, midpoint = 0.5, value = 7.28]
.. | | |--leaf "drat" ( value.drat = 3.6 )
.. | | `--leaf "gear" ( value.gear = 3.69 )
.. | `--[dendrogram w/ 2 branches and 2 members at h = 33.3, midpoint = 0.5, value = 37.9]
.. | |--leaf "qsec" ( value.qsec = 17.8 )
.. | `--leaf "mpg" ( value.mpg = 20.1 )
.. `--[dendrogram w/ 2 branches and 2 members at h = 657, midpoint = 0.5, value = 377]
.. |--leaf "hp" ( value.hp = 147 )
.. `--leaf "disp" ( value.disp = 231 )
$ breaks : num [1:257] -3.21 -3.19 -3.16 -3.14 -3.11 ...
$ col : chr [1:256] "#80FFFFFF" "#80FFFFFF" "#81FFFFFF" "#82FFFFFF" ...
$ vline : num 0
$ colorTable :'data.frame': 256 obs. of 3 variables:
..$ low : num [1:256] -3.21 -3.19 -3.16 -3.14 -3.11 ...
..$ high : num [1:256] -3.19 -3.16 -3.14 -3.11 -3.09 ...
..$ color: Factor w/ 254 levels "#80FFFFFF","#81FFFFFF",..: 1 1 2 3 4 5 6 7 8 9 ...
$ layout :List of 3
..$ lmat: num [1:3, 1:3] 6 0 4 0 0 1 5 2 3
..$ lhei: num [1:3] 1.5 0.2 4
..$ lwid: num [1:3] 1.5 0.2 4
> ## IGNORE_RDIFF_END
>
> ## Test row and column separators
> heatmap.2(x,dendrogram="col", colsep=1) ## one colsep
> heatmap.2(x,dendrogram="col", rowsep=1) ## one rowsep
>
> heatmap.2(x,dendrogram="col", colsep=1:2) ## two colseps
> heatmap.2(x,dendrogram="col", rowsep=1:2) ## two rowseps
>
> proc.time()
user system elapsed
1.190 0.064 1.245
|
