[R] remove quotes from matrix

[Bert Gunter]

Works fine for me. What do you object to in the following?

Calling the above df "d",

> dm <- as.matrix(d)
> dm
  Sub_Pathways            BMI_beta   SAT_beta   VAT_beta
1 "Alanine_and_Aspartate" " 0.23820" "-0.02409" " 0.94180"
2 "Alanine_and_Aspartate" "-0.31300" "-1.97510" "-2.22040"
3 "Alanine_and_Aspartate" " 0.12380" " 0.40950" " 0.68050"
4 "Alanine_and_Aspartate" " 0.30350" " 0.48610" " 0.70830"
5 "Alanine_and_Aspartate" "-0.00982" " 0.32930" " 0.01597"
  VSR_beta
1 " 0.24690"
2 "-0.23540"
3 " 0.05539"
4 " 0.01337"
5 "-0.04353"
> dimnames(dm)
[[1]]
[1] "1" "2" "3" "4" "5"

[[2]]
[1] "Sub_Pathways" "BMI_beta"     "SAT_beta"     "VAT_beta"
[5] "VSR_beta"

> dm <- noquote(dm)
> dm
  Sub_Pathways          BMI_beta SAT_beta VAT_beta VSR_beta
1 Alanine_and_Aspartate  0.23820 -0.02409  0.94180  0.24690
2 Alanine_and_Aspartate -0.31300 -1.97510 -2.22040 -0.23540
3 Alanine_and_Aspartate  0.12380  0.40950  0.68050  0.05539
4 Alanine_and_Aspartate  0.30350  0.48610  0.70830  0.01337
5 Alanine_and_Aspartate -0.00982  0.32930  0.01597 -0.04353
> dimnames(dm)
[[1]]
[1] "1" "2" "3" "4" "5"

[[2]]
[1] "Sub_Pathways" "BMI_beta"     "SAT_beta"     "VAT_beta"
[5] "VSR_beta"


Perhaps you need to read ?noquote or ?matrix.

-- Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Tue, Sep 19, 2017 at 8:20 AM, greg holly <mak.hholly at gmail.com> wrote:

> Dear all;
>
> Thanks. Here are the dput results as Duncan suggested.
>
> Regards,
>
> Greg
>
> structure(list(Sub_Pathways = structure(c(3L, 3L, 3L, 3L, 3L), .Label =
> c("Acetylated_Peptides",
> "Advanced_Glycation_End-product", "Alanine_and_Aspartate", "Aminosugar",
> "Ascorbate_and_Aldarate", "Carnitine", "Ceramides", "Creatine",
> "Diacylglycerol", "Dipeptide", "Dipeptide_Derivative",
> "Disaccharides_and_Oligosaccharides",
> "Eicosanoid", "Endocannabinoid", "Fatty_Acid(Acyl_Carnitine)",
> "Fatty_Acid(Acyl_Glycine)", "Fatty_Acid,_Amino", "Fatty_Acid,_Branched",
> "Fatty_Acid,_Dicarboxylate", "Fatty_Acid,_Dihydroxy",
> "Fatty_Acid,_Monohydroxy",
> "Fatty_Acid_(Acyl_Choline)", "Fatty_Acid_(Acyl_Glutamine)",
> "Fatty_Acid_(also_BCAA)",
> "Fatty_Acid_Synthesis", "Fibrinogen_Cleavage_Peptide",
> "Fructose,_Mannose_and_Galactose",
> "Gamma-glutamyl_Amino_Acid", "Glutamate", "Glutathione", "Glycerolipid",
> "Glycine,_Serine_and_Threonine", "Glycogen",
> "Glycolysis,_Gluconeogenesis,_and_Pyruvate",
> "Guanidino_and_Acetamido", "Hemoglobin_and_Porphyrin", "Histidine",
> "Inositol", "Ketone_Bodies", "Leucine,_Isoleucine_and_Valine",
> "Long_Chain_Fatty_Acid", "Lysine", "Lyso-phospho-ether", "Lysolipid",
> "Lysoplasmalogen", "Medium_Chain_Fatty_Acid",
> "Methionine,_Cysteine,_SAM_and_Taurine",
> "Mevalonate", "Monoacylglycerol", "Nicotinate_and_Nicotinamide",
> "Oxidative_Phosphorylation", "Pantothenate_and_CoA", "Pentose",
> "Phenylalanine_and_Tyrosine", "Phospholipid", "Plasmalogen",
> "Polyamine", "Polypeptide", "Polyunsaturated_Fatty_Acid_(n3_and_n6)",
> "Primary_Bile_Acid", "Purine,_(Hypo)Xanthine/Inosine_containing",
> "Purine,_Adenine_containing", "Purine,_Guanine_containing",
> "Pyrimidine,_Cytidine_containing",
> "Pyrimidine,_Orotate_containing", "Pyrimidine,_Thymine_containing",
> "Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid",
> "Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol",
> "TCA_Cycle", "Tocopherol", "Tryptophan",
> "Urea_cycle;_Arginine_and_Proline",
> "Vitamin_A", "Vitamin_B6"), class = "factor"), BMI_beta = c(0.2382,
> -0.313, 0.1238, 0.3035, -0.00982), SAT_beta = c(-0.02409, -1.9751,
> 0.4095, 0.4861, 0.3293), VAT_beta = c(0.9418, -2.2204, 0.6805,
> 0.7083, 0.01597), VSR_beta = c(0.2469, -0.2354, 0.05539, 0.01337,
> -0.04353)), .Names = c("Sub_Pathways", "BMI_beta", "SAT_beta",
> "VAT_beta", "VSR_beta"), row.names = c(NA, 5L), class = "data.frame")
>
> On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <murdoch.duncan at gmail.com
> >
> wrote:
>
> > On 19/09/2017 9:47 AM, greg holly wrote:
> >
> >> Hi all;
> >>
> >> I have data at 734*22 dimensions with rows and columns names are
> >> non-numeric.When I convert this data into matrix then all values show up
> >> with quotes. Then when I use
> >> x1= noquotes(x) to remove the quotes from the matrix then non-numeric
> row
> >> names remain all other values in matrix disappear.
> >>
> >> Your help is greatly appreciated.
> >>
> >>
> >
> > Matrices in R can have only one type.  If you start with a dataframe and
> > any columns contain character data, all entries will be converted to
> > character, and the matrix will be displayed with quotes.
> >
> > When you say all values disappear, it sounds as though you are displaying
> > strings containing nothing (or just blanks).  Those will be displayed as
> ""
> > normally, but if the matrix is marked to display without quotes, they are
> > displayed as empty strings, so it will appear that nothing is displayed.
> >
> > You can see the structure of the original data using the str() function,
> > e.g. str(x) should display types for each column.
> >
> > If this isn't enough to explain what's going on, please show us more
> > detail.  For example, show us the result of
> >
> > y <- x[1:5, 1:5]
> > dput(y)
> >
> > both before and after converting x to a matrix.
> >
> > Duncan Murdoch
> >
>
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>
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