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. Greg
remove quotes from matrix
9 messages · Duncan Murdoch, greg holly, Jeff Newmiller +2 more
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
Hi Duncan and Bert; I do appreciate for your replies. I just figured out that after x1= noquotes(x) commend my 733*22 matrix returns into n*1 vector. Is there way to keep this as matrix with the dimension of 733*22? Regards, Greg 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
Greg, I think you should stop using noquote, because it is doing something that will not be useful to you for preparing your data for analysis. Please follow Duncan's advice and provide us with a sample of your data. Also, please set your email program to send plain text rather than HTML formatted text.
Sent from my phone. Please excuse my brevity. On September 19, 2017 7:49:12 AM PDT, greg holly <mak.hholly at gmail.com> wrote: >Hi Duncan and Bert; > >I do appreciate for your replies. I just figured out that after x1= >noquotes(x) commend my 733*22 matrix returns into n*1 vector. Is there >way >to keep this as matrix with the dimension of 733*22? > >Regards, > >Greg > > >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 >> > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.
Your claims are false -- or at least confused.
d <- data.frame(a = I(letters[1:3]), b = 1:3)
## the I() is to prevent automatic conversion to factor
d
a b 1 a 1 2 b 2 3 c 3
dm <- as.matrix(d) dm
a b [1,] "a" "1" [2,] "b" "2" [3,] "c" "3"
dimnames(dm)
[[1]] NULL [[2]] [1] "a" "b" ## Note that there are no rownames, as d had none.
dm <- noquote(dm) dm
a b [1,] a 1 [2,] b 2 [3,] c 3 We still need a reprex to resolve the confusion. -- 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 7:49 AM, greg holly <mak.hholly at gmail.com> wrote:
Hi Duncan and Bert; I do appreciate for your replies. I just figured out that after x1= noquotes(x) commend my 733*22 matrix returns into n*1 vector. Is there way to keep this as matrix with the dimension of 733*22? Regards, Greg 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
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/ posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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
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
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/ posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Your description was confusing. You do not have row names that are non-numeric:
str(dta)
'data.frame': 5 obs. of 5 variables: $ Sub_Pathways: Factor w/ 79 levels "Acetylated_Peptides",..: 3 3 3 3 3 $ BMI_beta : num 0.2382 -0.313 0.1238 0.3035 -0.00982 $ SAT_beta : num -0.0241 -1.9751 0.4095 0.4861 0.3293 $ VAT_beta : num 0.942 -2.22 0.68 0.708 0.016 $ VSR_beta : num 0.2469 -0.2354 0.0554 0.0134 -0.0435 You have a column that is a factor with 79 levels. That cannot be row names because you indicated that the original data was 734*22 dimensions and row names cannot have duplications. If you want numeric values, you need to strip off the first column:
as.matrix(dta[ , -1])
BMI_beta SAT_beta VAT_beta VSR_beta 1 0.23820 -0.02409 0.94180 0.24690 2 -0.31300 -1.97510 -2.22040 -0.23540 3 0.12380 0.40950 0.68050 0.05539 4 0.30350 0.48610 0.70830 0.01337 5 -0.00982 0.32930 0.01597 -0.04353 If you just want to print the character values without quotes:
print(as.matrix(dta), quote=FALSE)
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
But do not forget that they are still character strings.
----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg holly
Sent: Tuesday, September 19, 2017 10:21 AM
To: Duncan Murdoch <murdoch.duncan at gmail.com>
Cc: r-help mailing list <r-help at r-project.org>
Subject: Re: [R] remove quotes from matrix
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
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hi Bert; I sincerely appreciate for this. When I follow your way I have got dimnames(dm) [[1]] NULL I think this is the reason why the matrix is being converted into a column vector. Regards, Greg On Tue, Sep 19, 2017 at 11:32 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote:
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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