Dear R user,
I want to reshape a long data frame to wide format, I made the following example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j");
df.long <-data.frame(sample, marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
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non-standard reshape from long to wide
7 messages · Yuan Chun Ding, Bert Gunter, Rui Barradas +1 more
Is this homework? There is a no-homework policy on this list. If not, note that you are usually asked to show what you tried and the error messages you received. 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 Thu, Jan 7, 2021 at 10:40 AM Yuan Chun Ding <ycding at coh.org> wrote:
Dear R user,
I want to reshape a long data frame to wide format, I made the following
example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j");
df.long <-data.frame(sample, marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or
entity to which they are addressed. This communication may contain
information that is privileged, confidential, or exempt from disclosure
under applicable law (e.g., personal health information, research data,
financial information). Because this e-mail has been sent without
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view the information, forward it to others or tamper with the information
without the knowledge or consent of the sender. If you are not the intended
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in error, please notify the sender immediately by replying to this message
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sender that you do not wish to receive further e-mail from the sender.
(LCP301)
______________________________________________ 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,
No, this Is not home work related. Original data have 87352 rows. I used the standard reshape function and got warning message. So I reformatted the wide format to meet my research purpose.
mut2 <-mut[,c("Tumor_Sample_Barcode","mut.id", "Hugo_Symbol")]
mut2 <-mut2[order(mut2$Hugo_Symbol),]
mut3 <-mut2[!duplicated(mut2),]
mut4 <-reshape(mut3, idvar = "Hugo_Symbol", timevar = "Tumor_Sample_Barcode", direction = "wide")
There were 50 or more warnings (use warnings() to see the first 50)
View(mut4) warnings()
Warning messages: 1: In reshapeWide(data, idvar = idvar, timevar = timevar, ... : multiple rows match for Tumor_Sample_Barcode=TCGA-A8-A09Z-01A-11W-A019-09: first taken 2: In reshapeWide(data, idvar = idvar, timevar = timevar, ... : From: Bert Gunter [mailto:bgunter.4567 at gmail.com] Sent: Thursday, January 7, 2021 10:52 AM To: Yuan Chun Ding <ycding at coh.org> Cc: r-help at r-project.org Subject: Re: [R] non-standard reshape from long to wide Is this homework? There is a no-homework policy on this list. If not, note that you are usually asked to show what you tried and the error messages you received. 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 Thu, Jan 7, 2021 at 10:40 AM Yuan Chun Ding <ycding at coh.org<mailto:ycding at coh.org>> wrote:
Dear R user,
I want to reshape a long data frame to wide format, I made the following example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j");
df.long <-data.frame(sample, marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
______________________________________________
R-help at r-project.org<mailto:R-help at r-project.org> mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-help__;!!Fou38LsQmgU!8Xh6f5YkEhmPfDyrfZAdBKkVH3I-iNCUoXNhMSZyF6JgRliIYBMD4tWItfuZ$>
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<https://urldefense.com/v3/__http:/www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!8Xh6f5YkEhmPfDyrfZAdBKkVH3I-iNCUoXNhMSZyF6JgRliIYBMD4qvlyPfu$>
and provide commented, minimal, self-contained, reproducible code.
Show us your attempt on your example data. Also note that warnings are *not* errors, though they typically do indicate problems. -- Bert
On Thu, Jan 7, 2021 at 11:09 AM Yuan Chun Ding <ycding at coh.org> wrote:
Hi Bert,
No, this Is not home work related. Original data have 87352 rows. I used
the standard reshape function and got warning message. So I reformatted the
wide format to meet my research purpose.
mut2 <-mut[,c("Tumor_Sample_Barcode","mut.id", "Hugo_Symbol")]
mut2 <-mut2[order(mut2$Hugo_Symbol),]
mut3 <-mut2[!duplicated(mut2),]
mut4 <-reshape(mut3, idvar = "Hugo_Symbol", timevar =
"Tumor_Sample_Barcode", direction = "wide")
There were 50 or more warnings (use warnings() to see the first 50)
View(mut4)
warnings()
Warning messages:
1: In reshapeWide(data, idvar = idvar, timevar = timevar, ... :
multiple rows match for
Tumor_Sample_Barcode=TCGA-A8-A09Z-01A-11W-A019-09: first taken
2: In reshapeWide(data, idvar = idvar, timevar = timevar, ... :
*From:* Bert Gunter [mailto:bgunter.4567 at gmail.com]
*Sent:* Thursday, January 7, 2021 10:52 AM
*To:* Yuan Chun Ding <ycding at coh.org>
*Cc:* r-help at r-project.org
*Subject:* Re: [R] non-standard reshape from long to wide
Is this homework? There is a no-homework policy on this list.
If not, note that you are usually asked to show what you tried and the
error messages you received.
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 Thu, Jan 7, 2021 at 10:40 AM Yuan Chun Ding <ycding at coh.org> wrote:
Dear R user,
I want to reshape a long data frame to wide format, I made the following
example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j");
df.long <-data.frame(sample, marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or
entity to which they are addressed. This communication may contain
information that is privileged, confidential, or exempt from disclosure
under applicable law (e.g., personal health information, research data,
financial information). Because this e-mail has been sent without
encryption, individuals other than the intended recipient may be able to
view the information, forward it to others or tamper with the information
without the knowledge or consent of the sender. If you are not the intended
recipient, or the employee or person responsible for delivering the message
to the intended recipient, any dissemination, distribution or copying of
the communication is strictly prohibited. If you received the communication
in error, please notify the sender immediately by replying to this message
and deleting the message and any accompanying files from your system. If,
due to the security risks, you do not wish to receive further
communications via e-mail, please reply to this message and inform the
sender that you do not wish to receive further e-mail from the sender.
(LCP301)
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help <https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/r-help__;!!Fou38LsQmgU!8Xh6f5YkEhmPfDyrfZAdBKkVH3I-iNCUoXNhMSZyF6JgRliIYBMD4tWItfuZ$> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html <https://urldefense.com/v3/__http:/www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!8Xh6f5YkEhmPfDyrfZAdBKkVH3I-iNCUoXNhMSZyF6JgRliIYBMD4qvlyPfu$> and provide commented, minimal, self-contained, reproducible code.
Hello,
Here is a dplyr solution. The main trick is to create a column of 1's,
then pipe to pivot_wider.
library(dplyr)
library(tidyr)
df.long %>%
mutate(values = 1) %>%
pivot_wider(
id_cols = sample,
names_from = marker,
values_from = values,
values_fill = NA
)
Note: your df.wide is not a data.frame, the transpose coerces it to
matrix. In this case it doesn't matter because it was just an example of
expected output but in other, real use cases you must be careful.
df.wide <- as.data.frame(df.wide)
would solve it.
Hope this helps,
Rui Barradas
?s 18:39 de 07/01/21, Yuan Chun Ding escreveu:
Dear R user,
I want to reshape a long data frame to wide format, I made the following example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j");
df.long <-data.frame(sample, marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
______________________________________________ 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 Rui,
Thank you so much!! You code works well and I am looking into the pivot_wider function.
Yuan Ding
-----Original Message-----
From: Rui Barradas [mailto:ruipbarradas at sapo.pt]
Sent: Thursday, January 7, 2021 12:19 PM
To: Yuan Chun Ding <ycding at coh.org>; r-help at r-project.org
Subject: Re: [R] non-standard reshape from long to wide
Hello,
Here is a dplyr solution. The main trick is to create a column of 1's, then pipe to pivot_wider.
library(dplyr)
library(tidyr)
df.long %>%
mutate(values = 1) %>%
pivot_wider(
id_cols = sample,
names_from = marker,
values_from = values,
values_fill = NA
)
Note: your df.wide is not a data.frame, the transpose coerces it to
matrix. In this case it doesn't matter because it was just an example of
expected output but in other, real use cases you must be careful.
df.wide <- as.data.frame(df.wide)
would solve it.
Hope this helps,
Rui Barradas
?s 18:39 de 07/01/21, Yuan Chun Ding escreveu:
Dear R user,
I want to reshape a long data frame to wide format, I made the following example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j");
df.long <-data.frame(sample, marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!Fou38LsQmgU!9ccbhtYzBJoahdschhouzo2kkluOs-EdoH8jn32fv9E22xaJ4GzfrI0bOvVl$ PLEASE do read the posting guide https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!Fou38LsQmgU!9ccbhtYzBJoahdschhouzo2kkluOs-EdoH8jn32fv9E22xaJ4GzfrKjC2095$ and provide commented, minimal, self-contained, reproducible code.
Hi
dcast from reshape is close, however column order is different
mydf <- dcast(df.long, sample~marker)
(!is.na(mydf[,-1]))*1
g j k u x y
[1,] 1 0 1 0 1 0
[2,] 0 1 0 1 1 1
[3,] 0 0 0 0 1 1
You just need to change 0 to NA and add rownames from mydf.
Cheers
Petr
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Yuan Chun Ding
Sent: Thursday, January 7, 2021 7:40 PM
To: r-help at r-project.org
Subject: [R] non-standard reshape from long to wide
Dear R user,
I want to reshape a long data frame to wide format, I made the following
example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy" , "uy");
marker <-
c("x" , "y" , "g" , "x" , "k" , "y" , "x" , "u" , "j"); df.long
<-data.frame(sample,
marker);
xr <-c(1,1,NA,NA,NA,NA);
fh <-c(1,NA,1,1,NA,NA);
uy <-c(1,1,NA,NA,1,1);
df.wide <- t(data.frame(xr,fh,uy));
colnames(df.wide)<-c("x","y","g","k", "u","j");
----------------------------------------------------------------------
------------------------------------------------------------
-SECURITY/CONFIDENTIALITY WARNING-
This message and any attachments are intended solely for the individual or
entity to which they are addressed. This communication may contain
information that is privileged, confidential, or exempt from disclosure
under
applicable law (e.g., personal health information, research data,
financial
information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without
the
knowledge or consent of the sender. If you are not the intended recipient,
or
the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message
and
deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications
via
e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
______________________________________________ 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.