[R] log transform a data frame

[Ana Marija]

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
>>
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