[R] Fwd: Re: transpose and split dataframe
Matthew
mccorm@ck @end|ng |rom mo|b|o@mgh@h@rv@rd@edu
Mon May 6 22:12:42 CEST 2019
Thank you very much Jim and David for your scripts and accompanying
explanations.
I was intrigued at the results that came from David's script. As seen
below where I have taken a small piece of his DataTable:
AT1G69490 AT1G29860 AT4G18170 *AT5G46350*
AT1G01560 0 0 0 1
*AT1G02920* 1 2 2 4
AT1G02930 1 2 2 4
AT1G05675 1 1 1 2
There are numbers other than 1 or 0, which was not what I was
expecting. The data I am working with come from downloading results of
an analysis done at a particular web site. I looked at Jim's solution,
and the equivalent of the above would be:
AT1G69490 _AT1G29860_ _AT1G29860_ AT4G18170 AT4G18170
*AT5G46350 AT5G46350 AT5G46350 AT5G46350 AT5G46350*
AT1G01560 NA NA NA NA NA NA NA NA AT1G01560 NA
*AT1G02920* AT1G02920 AT1G02920 AT1G02920 AT1G02920
AT1G02920 AT1G02920 AT1G02920 AT1G02920 AT1G02920 NA
AT1G02930 AT1G02930 AT1G02930 AT1G02930 AT1G02930
AT1G02930 AT1G02930 AT1G02930 AT1G02930 AT1G02930 NA
AT1G05675 AT1G05675 AT1G05675 NA AT1G05675 NA
AT1G05675 AT1G05675 NA NA NA
The above is the format that I was desiring, but I was not expecting
that a single ATG number would be the name of multiple columns. As shown
above, _AT1G2960_ is the name of two columns and *AT5G46350* is the name
of 5 columns (You may have to widen the e-mail across the screen to see
it clearly). When a single ATG number, such as AT5G46350, names multiple
columns, then the contents of each of those columns may or may not be
the same. For example, going across a single row looking at *AT1G02920*,
it occurs in the first column, hence the 1 in David's DataTable. It
occurs in both AT1G29860 columns, hence the 2 in the DataTable. It again
occurs in both AT4G18170 columns, so another 2 in the DataTable, and
finally it occurs in only 4 of the 5 AT5G46350 columns, so the 4 in the
DataTable.
When the same ATG number names multiple columns it is because
different methods were used to determine the content of each column. So,
if an ATG number such as AT1G05675 occurs in all columns with the same
name, I then know that it was by multiple methods that this has been
shown, and if it only occurs in some of the columns, I know that all
methods did not associate it with the column name ATG. David's result
complements Jim's, and both end up being very helpful to me.
Thanks again to both of you for your time and help.
Matthew
On 5/2/2019 8:40 PM, Jim Lemon wrote:
> External Email - Use Caution
>
> Hi again,
> Just noticed that the NA fill in the original solution is unnecessary, thus:
>
> # split the second column at the commas
> hitsplit<-strsplit(mmdf$hits,",")
> # get all the sorted hits
> allhits<-sort(unique(unlist(hitsplit)))
> tmmdf<-as.data.frame(matrix(NA,ncol=length(hitsplit),nrow=length(allhits)))
> # change the names of the list
> names(tmmdf)<-mmdf$Regulator
> for(column in 1:length(hitsplit)) {
> hitmatches<-match(hitsplit[[column]],allhits)
> hitmatches<-hitmatches[!is.na(hitmatches)]
> tmmdf[hitmatches,column]<-allhits[hitmatches]
> }
>
> Jim
>
> On Fri, May 3, 2019 at 10:32 AM Jim Lemon <drjimlemon using gmail.com> wrote:
>> Hi Matthew,
>> I'm not sure whether you want something like your initial request or
>> David's solution. The result of this can be transformed into the
>> latter:
>>
>> mmdf<-read.table(text="Regulator hits
>> AT1G69490 AT4G31950,AT5G24110,AT1G26380,AT1G05675,AT3G12910,AT5G64905,AT1G22810,AT1G79680,AT3G02840,AT5G25260,AT5G57220,AT2G37430,AT2G26560,AT1G56250,AT3G23230,AT1G16420,AT1G78410,AT4G22030,AT5G05300,AT1G69930,AT4G03460,AT4G11470,AT5G25250,AT5G36925,AT2G30750,AT1G16150,AT1G02930,AT2G19190,AT4G11890,AT1G72520,AT4G31940,AT5G37490,AT5G52760,AT5G66020,AT3G57460,AT4G23220,AT3G15518,AT2G43620,AT2G02010,AT1G35210,AT5G46295,AT1G17147,AT1G11925,AT2G39200,AT1G02920,AT2G40180,AT1G59865,AT4G35180,AT4G15417,AT1G51820,AT1G06135,AT1G36622,AT5G42830
>> AT1G29860 AT4G31950,AT5G24110,AT1G05675,AT3G12910,AT5G64905,AT1G22810,AT1G14540,AT1G79680,AT1G07160,AT3G23250,AT5G25260,AT1G53625,AT5G57220,AT2G37430,AT3G54150,AT1G56250,AT3G23230,AT1G16420,AT1G78410,AT4G22030,AT1G69930,AT4G03460,AT4G11470,AT5G25250,AT5G36925,AT4G14450,AT2G30750,AT1G16150,AT1G02930,AT2G19190,AT4G11890,AT1G72520,AT4G31940,AT5G37490,AT4G08555,AT5G66020,AT5G26920,AT3G57460,AT4G23220,AT3G15518,AT2G43620,AT1G35210,AT5G46295,AT1G17147,AT1G11925,AT2G39200,AT1G02920,AT4G35180,AT4G15417,AT1G51820,AT4G40020,AT1G06135
>> AT1G2986 AT5G64905,AT1G21120,AT1G07160,AT5G25260,AT1G53625,AT1G56250,AT2G31345,AT4G11170,AT1G66090,AT1G26410,AT3G55840,AT1G69930,AT4G03460,AT5G25250,AT5G36925,AT1G26420,AT5G42380,AT1G16150,AT2G22880,AT1G02930,AT4G11890,AT1G72520,AT5G66020,AT2G43620,AT2G44370,AT4G15975,AT1G35210,AT5G46295,AT1G11925,AT2G39200,AT1G02920,AT4G14370,AT4G35180,AT4G15417,AT2G18690,AT5G11140,AT1G06135,AT5G42830",
>> header=TRUE,stringsAsFactors=FALSE)
>> # split the second column at the commas
>> hitsplit<-strsplit(mmdf$hits,",")
>> # define a function that will fill with NAs
>> NAfill<-function(x,n) return(x[1:n])
>> # get the maximum length of hits
>> maxlen<-max(unlist(lapply(hitsplit,length)))
>> # fill the list with NAs
>> hitsplit<-lapply(hitsplit,NAfill,maxlen)
>> # get all the sorted hits
>> allhits<-sort(unique(unlist(hitsplit)))
>> tmmdf<-as.data.frame(matrix(NA,ncol=length(hitsplit),nrow=length(allhits)))
>> # change the names of the list
>> names(tmmdf)<-mmdf$Regulator
>> # replace all NA values in tmmdf where they appear in hitsplit
>> for(column in 1:length(hitsplit)) {
>> hitmatches<-match(hitsplit[[column]],allhits)
>> hitmatches<-hitmatches[!is.na(hitmatches)]
>> tmmdf[hitmatches,column]<-allhits[hitmatches]
>> }
>>
>> Jim
>>
>> On Fri, May 3, 2019 at 12:43 AM David L Carlson <dcarlson using tamu.edu> wrote:
>>> We still have only the toy version of your data from your first email. The second email used dput() as I suggested, but you truncated the results so it is useless for testing purposes.
>>>
>>> Use the following code after creating DataList (up to mx <- ... ) in my earlier answer:
>>>
>>> n <- sapply(DataList, length)
>>> hits <- unname(unlist(DataList))
>>> Regulator <- unname(unlist(mapply(rep, names(DataList), times=n)))
>>> DataTable <- table(hits, Regulator)
>>>
>>> # Regulator
>>> # hits AT1G69490 AT2G55980
>>> # AT1G05675 1 0
>>> # AT1G26380 1 0
>>> # AT2G85403 0 1
>>> # AT4G31950 1 0
>>> # AT4G89223 0 1
>>> # AT5G24110 1 0
>>>
>>> Now the Regulators and the hits will be listed in alphabetical order. The table has 0's for Regulators that do not have a particular hit. If you want NAs:
>>>
>>> DataTable[DataTable==0] <- NA
>>> print(DataTable, na.print="NA")
>>> # Regulator
>>> # hits AT1G69490 AT2G55980
>>> # AT1G05675 1 NA
>>> # AT1G26380 1 NA
>>> # AT2G85403 NA 1
>>> # AT4G31950 1 NA
>>> # AT4G89223 NA 1
>>> # AT5G24110 1 NA
>>>
>>> If you need a data frame instead of a table:
>>>
>>> as.data.frame.matrix(DataTable)
>>>
>>> ----------------------------------------
>>> David L Carlson
>>> Department of Anthropology
>>> Texas A&M University
>>> College Station, TX 77843-4352
>>>
>>> -----Original Message-----
>>> From: R-help <r-help-bounces using r-project.org> On Behalf Of Matthew
>>> Sent: Tuesday, April 30, 2019 4:31 PM
>>> To: r-help using r-project.org
>>> Subject: [R] Fwd: Re: transpose and split dataframe
>>>
>>> Thanks for your reply. I was trying to simplify it a little, but must
>>> have got it wrong. Here is the real dataframe, TF2list:
>>>
>>> str(TF2list)
>>> 'data.frame': 152 obs. of 2 variables:
>>> $ Regulator: Factor w/ 87 levels "AT1G02065","AT1G13960",..: 17 6 6 54
>>> 54 82 82 82 82 82 ...
>>> $ hits : Factor w/ 97 levels
>>> "AT1G05675,AT3G12910,AT1G22810,AT1G14540,AT1G21120,AT1G07160,AT5G22520,AT1G56250,AT2G31345,AT5G22530,AT4G11170,A"|
>>> __truncated__,..: 65 57 90 57 87 57 56 91 31 17 ...
>>>
>>> And the first few lines resulting from dput(head(TF2list)):
>>>
>>> dput(head(TF2list))
>>> structure(list(Regulator = structure(c(17L, 6L, 6L, 54L, 54L,
>>> 82L), .Label = c("AT1G02065", "AT1G13960", "AT1G18860", "AT1G23380",
>>> "AT1G29280", "AT1G29860", "AT1G30650", "AT1G55600", "AT1G62300",
>>> "AT1G62990", "AT1G64000", "AT1G66550", "AT1G66560", "AT1G66600",
>>> "AT1G68150", "AT1G69310", "AT1G69490", "AT1G69810", "AT1G70510", ...
>>>
>>> This is another way of looking at the first 4 entries (Regulator is
>>> tab-separated from hits):
>>>
>>> Regulator
>>> hits
>>> 1
>>> AT1G69490
>>> AT4G31950,AT5G24110,AT1G26380,AT1G05675,AT3G12910,AT5G64905,AT1G22810,AT1G79680,AT3G02840,AT5G25260,AT5G57220,AT2G37430,AT2G26560,AT1G56250,AT3G23230,AT1G16420,AT1G78410,AT4G22030,AT5G05300,AT1G69930,AT4G03460,AT4G11470,AT5G25250,AT5G36925,AT2G30750,AT1G16150,AT1G02930,AT2G19190,AT4G11890,AT1G72520,AT4G31940,AT5G37490,AT5G52760,AT5G66020,AT3G57460,AT4G23220,AT3G15518,AT2G43620,AT2G02010,AT1G35210,AT5G46295,AT1G17147,AT1G11925,AT2G39200,AT1G02920,AT2G40180,AT1G59865,AT4G35180,AT4G15417,AT1G51820,AT1G06135,AT1G36622,AT5G42830
>>> 2
>>> AT1G29860
>>> AT4G31950,AT5G24110,AT1G05675,AT3G12910,AT5G64905,AT1G22810,AT1G14540,AT1G79680,AT1G07160,AT3G23250,AT5G25260,AT1G53625,AT5G57220,AT2G37430,AT3G54150,AT1G56250,AT3G23230,AT1G16420,AT1G78410,AT4G22030,AT1G69930,AT4G03460,AT4G11470,AT5G25250,AT5G36925,AT4G14450,AT2G30750,AT1G16150,AT1G02930,AT2G19190,AT4G11890,AT1G72520,AT4G31940,AT5G37490,AT4G08555,AT5G66020,AT5G26920,AT3G57460,AT4G23220,AT3G15518,AT2G43620,AT1G35210,AT5G46295,AT1G17147,AT1G11925,AT2G39200,AT1G02920,AT4G35180,AT4G15417,AT1G51820,AT4G40020,AT1G06135
>>>
>>> 3
>>> AT1G2986
>>> AT5G64905,AT1G21120,AT1G07160,AT5G25260,AT1G53625,AT1G56250,AT2G31345,AT4G11170,AT1G66090,AT1G26410,AT3G55840,AT1G69930,AT4G03460,AT5G25250,AT5G36925,AT1G26420,AT5G42380,AT1G16150,AT2G22880,AT1G02930,AT4G11890,AT1G72520,AT5G66020,AT2G43620,AT2G44370,AT4G15975,AT1G35210,AT5G46295,AT1G11925,AT2G39200,AT1G02920,AT4G14370,AT4G35180,AT4G15417,AT2G18690,AT5G11140,AT1G06135,AT5G42830
>>>
>>> So, the goal would be to
>>>
>>> first: Transpose the existing dataframe so that the factor Regulator
>>> becomes a column name (column 1 name = AT1G69490, column2 name
>>> AT1G29860, etc.) and the hits associated with each Regulator become
>>> rows. Hits is a comma separated 'list' ( I do not not know if
>>> technically it is an R list.), so it would have to be comma
>>> 'unseparated' with each entry becoming a row (col 1 row 1 = AT4G31950,
>>> col 1 row 2 - AT5G24410, etc); like this :
>>>
>>> AT1G69490
>>> AT4G31950
>>> AT5G24110
>>> AT1G05675
>>> AT5G64905
>>>
>>> ... I did not include all the rows)
>>>
>>> I think it would be best to actually make the first entry a separate
>>> dataframe ( 1 column with name = AT1G69490 and number of rows depending
>>> on the number of hits), then make the second column (column name =
>>> AT1G29860, and number of rows depending on the number of hits) into a
>>> new dataframe and do a full join of of the two dataframes; continue by
>>> making the third column (column name = AT1G2986) into a dataframe and
>>> full join it with the previous; continue for the 152 observations so
>>> that then end result is a dataframe with 152 columns and number of rows
>>> depending on the entry with the greatest number of hits. The full joins
>>> I can do with dplyr, but getting up to that point seems rather difficult.
>>>
>>> This would get me what my ultimate goal would be; each Regulator is a
>>> column name (152 columns) and a given row has either NA or the same hit.
>>>
>>> This seems very difficult to me, but I appreciate any attempt.
>>>
>>> Matthew
>>>
>>> On 4/30/2019 4:34 PM, David L Carlson wrote:
>>>> External Email - Use Caution
>>>>
>>>> I think we need more information. Can you give us the structure of the data with str(YourDataFrame). Alternatively you could copy a small piece into your email message by copying and pasting the results of the following code:
>>>>
>>>> dput(head(YourDataFrame))
>>>>
>>>> The data frame you present could not be a data frame since you say "hits" is a factor with a variable number of elements. If each value of "hits" was a single character string, it would only have 2 factor levels not 6 and your efforts to parse the string would make more sense. Transposing to a data frame would only be possible if each column was padded with NAs to make them equal in length. Since your example tries use the name TF2list, it is possible that you do not have a data frame but a list and you have no factor levels, just character vectors.
>>>>
>>>> If you are not familiar with R, it may be helpful to tell us what your overall goal is rather than an intermediate step. Very likely R can easily handle what you want by doing things a different way.
>>>>
>>>> ----------------------------------------
>>>> David L Carlson
>>>> Department of Anthropology
>>>> Texas A&M University
>>>> College Station, TX 77843-4352
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: R-help<r-help-bounces using r-project.org> On Behalf Of Matthew
>>>> Sent: Tuesday, April 30, 2019 2:25 PM
>>>> To: r-help (r-help using r-project.org)<r-help using r-project.org>
>>>> Subject: [R] transpose and split dataframe
>>>>
>>>> I have a data frame that is a lot bigger but for simplicity sake we can
>>>> say it looks like this:
>>>>
>>>> Regulator hits
>>>> AT1G69490 AT4G31950,AT5G24110,AT1G26380,AT1G05675
>>>> AT2G55980 AT2G85403,AT4G89223
>>>>
>>>> In other words:
>>>>
>>>> data.frame : 2 obs. of 2 variables
>>>> $Regulator: Factor w/ 2 levels
>>>> $hits : Factor w/ 6 levels
>>>>
>>>> I want to transpose it so that Regulator is now the column headings
>>>> and each of the AGI numbers now separated by commas is a row. So,
>>>> AT1G69490 is now the header of the first column and AT4G31950 is row 1
>>>> of column 1, AT5G24110 is row 2 of column 1, etc. AT2G55980 is header of
>>>> column 2 and AT2G85403 is row 1 of column 2, etc.
>>>>
>>>> I have tried playing around with strsplit(TF2list[2:2]) and
>>>> strsplit(as.character(TF2list[2:2]), but I am getting nowhere.
>>>>
>>>> Matthew
>>>>
>>>> ______________________________________________
>>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
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>>>
>>> ______________________________________________
>>> R-help using 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.
>>> ______________________________________________
>>> R-help using 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.
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