[R] log transform a data frame

[David Carlson]

Try this
pdf("~/graph.pdf")
par(mar=c(8, 4, 4, 2))
barplot(d2, legend= c("SYCL", "CUDA"), beside=
TRUE,las=2,cex.axis=0.7,cex.names=0.7,ylim=c(0,80), col=c("#9e9ac8",
"#6a51a3"))
dev.off()

See ?par to see the details for adjusting margins and other plot features.

David


On Tue, Jun 13, 2023 at 5:20 PM Ana Marija <sokovic.anamarija using gmail.com>
wrote:

> Thank you so much David, here is correction: d1=suppressWarnings(read.
> csv("/Users/anamaria/Downloads/B1. csv", stringsAsFactors=FALSE,
> header=TRUE)) d1$X <- NULL d2=as. matrix(sapply(d1, as. numeric))
> pdf("~/graph. pdf")b<-barplot(d2,
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
>
> ZjQcmQRYFpfptBannerEnd
> Thank you so much David, here is correction:
>
> d1=suppressWarnings(read.csv("/Users/anamaria/Downloads/B1.csv",
> stringsAsFactors=FALSE, header=TRUE))
> d1$X <- NULL
> d2=as.matrix(sapply(d1, as.numeric))
> pdf("~/graph.pdf")
> b<-barplot(d2, legend= c("SYCL", "CUDA"), beside=
> TRUE,las=2,cex.axis=0.7,cex.names=0.7,ylim=c(0,80), col=c("#9e9ac8",
> "#6a51a3"))
> dev.off()
>
>  > dput(head(d1))
> structure(list(Domain.decomp. = c("2. 1", "2"), DD.com..load = c(0L,
> 0L), Neighbor.search = c("3.7", "3. 1"), Launch.PP.GPU.ops. = c("0. 1",
> "0"), Comm..coord. = c("1 .6", "1 .0"), Force = c("1 . 5", "1 .2"
> ), Wait...Comm..F = c("1 .3", "1 .7"), PIE.mesh = c(65.6, 70.9
> ), Wait.Bonded.GPU = c(0L, 0L), wait.GPU.NB.nonloc. = c(0L, 0L
> ), Wait.GPU.NB.local = c(0L, 0L), NB.X.F.buffer.ops. = c(7.3,
> 4.4), Write.traje = c(0.3, 0.3), Update = c(6.3, 4.3), Constraints =
> c(8.9,
> 9.7), Comm..energies = c(0.9, 0.9), PIE.redist..X.F = c("8. 1",
> "8.7"), PIE.spread = c(29.7, 30.6), PIE.gather = c("19.9", "21 .3"
> ), PIE.3D.FFT = c(6, 8.6), PIE.3D.FFT.comm. = c("1 .2", "1 .0"
> ), PIE.solve.Elec = c(0.7, 0.5)), row.names = 1:2, class = "data.frame")
>
> Now my problem is that when I save my plot as PDF my labels on X axis are
> cut off. Any advice about that?
>
>
>
> On Tue, Jun 13, 2023 at 5:14 PM David Carlson <dcarlson using tamu.edu> wrote:
>
>> Your first data column appears to contain character data (e.g. SYCL) which
>> cannot be converted to numeric. You also appear to have 0's in the numeric
>> columns which will cause problems since log(0) is -Inf. Barplots are useful
>> for categorical data, but not continuous, numeric data which are better
>> handled with box plots or strip charts.
>>
>> Do not use printouts of your data since it hides important information.
>> Use str(a11) and dput(a11) or dput(head(a11)) to provide useful information
>> about your data.
>>
>> David L Carlson
>> Texas A&M University
>>
>>
>> On Tue, Jun 13, 2023 at 4:08 PM Ana Marija <sokovic.anamarija using gmail.com>
>> wrote:
>>
>>> Hello, I have a data frame like this: d11=suppressWarnings(read.
>>> csv("/Users/anamaria/Downloads/B1. csv", stringsAsFactors=FALSE,
>>> header=TRUE)) > d11 X Domain. decomp. DD. com. . load Neighbor. search
>>> Launch. PP. GPU. ops. Comm. . coord. 1 SYCL 2. 1
>>> ZjQcmQRYFpfptBannerStart
>>> This Message Is From an External Sender
>>> This message came from outside your organization.
>>>
>>> ZjQcmQRYFpfptBannerEnd
>>>
>>> Hello,
>>>
>>> I have a data frame like this:
>>>
>>> d11=suppressWarnings(read.csv("/Users/anamaria/Downloads/B1.csv",
>>> stringsAsFactors=FALSE, header=TRUE))
>>>
>>> > d11
>>>      X Domain.decomp. DD.com..load Neighbor.search Launch.PP.GPU.ops.
>>> Comm..coord.
>>> 1 SYCL           2. 1            0             3.7               0. 1
>>>   1 .6
>>> 2 CUDA              2            0            3. 1                  0
>>>   1 .0
>>>   Force Wait...Comm..F PIE.mesh Wait.Bonded.GPU wait.GPU.NB.nonloc.
>>> 1 1 . 5           1 .3     65.6               0                   0
>>> 2  1 .2           1 .7     70.9               0                   0
>>>   Wait.GPU.NB.local NB.X.F.buffer.ops. Write.traje Update Constraints
>>> Comm..energies
>>> 1                 0                7.3         0.3    6.3         8.9
>>>      0.9
>>> 2                 0                4.4         0.3    4.3         9.7
>>>      0.9
>>>   PIE.redist..X.F PIE.spread PIE.gather PIE.3D.FFT PIE.3D.FFT.comm.
>>> PIE.solve.Elec
>>> 1            8. 1       29.7       19.9        6.0             1 .2
>>>    0.7
>>> 2             8.7       30.6      21 .3        8.6             1 .0
>>>    0.5
>>>
>>> I am trying to log transform the whole data frame, but I get this error:
>>>
>>> > d1=log(d11)
>>> Error in Math.data.frame(d11) :
>>>   non-numeric variable(s) in data frame: X, Domain.decomp.,
>>> Neighbor.search, Launch.PP.GPU.ops., Comm..coord., Force, Wait...Comm..F,
>>> PIE.redist..X.F, PIE.gather, PIE.3D.FFT.comm
>>>
>>>
>>> My goal is to make a stacked barplot like this:
>>> d2=as.matrix(sapply(d1, as.numeric))
>>> b<-barplot(d2, legend= rownames(data2), beside=
>>> TRUE,las=2,cex.axis=0.7,cex.names=0.7,ylim=c(0,80), col=c("#9e9ac8",
>>> "#6a51a3"))
>>>
>>> If I don't log transform  my code runs.
>>>
>>> Please advise,
>>> Ana
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> ______________________________________________R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, seehttps://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!GkOclaf0NPpoVxF8zs_a2pCGlBelsouhJKKR4wG4cG_gEycZ6t-N6nbPvxD1AxnYureFFthr_Nc-zXCU0czR4zGIstg$
>>> PLEASE do read the posting guide https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!GkOclaf0NPpoVxF8zs_a2pCGlBelsouhJKKR4wG4cG_gEycZ6t-N6nbPvxD1AxnYureFFthr_Nc-zXCU0czRLvLqcYM$
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>

	[[alternative HTML version deleted]]