[R] Violin plots in R

[pooja sinha]

Hi All,

I need your help in making the violin plot in R using the data which is
attached herewith. I am new to R and having issues in tidying my data for
R. I am trying the code but I am not able to tidy my data for violin plot
in ggplot.

Any help will be highly appreciated.

Thanks,
Puja
__
R-help@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.

Re: [R] Need in formatting data for circos plot

[pooja sinha]

Thanks, the code is working now but it is not plotting in the colorwise
manner ie, khaki4 and indian red. Maybe I need to work more. If you have
any clue then please let me know.


Thanks again,
Puja

On Tue, Oct 5, 2021 at 9:19 AM PIKAL Petr  wrote:

> Hm,
>
> Maybe if you change
> > C(-7, 7)
> Error in C(-7, 7) : object not interpretable as a factor
>
> to
>
> > c(-7, 7)
> [1] -7  7
>
> Cheers
> Petr
>
>
> S pozdravem | Best Regards
> RNDr. Petr PIKAL
> Vedoucí Výzkumu a vývoje | Research Manager
> PRECHEZA a.s.
> nábř. Dr. Edvarda Beneše 1170/24 | 750 02 Přerov | Czech Republic
> Tel: +420 581 252 256 | GSM: +420 724 008 364
> petr.pi...@precheza.cz | www.precheza.cz
> Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních
> partnerů PRECHEZA a.s. jsou zveřejněny na:
> https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about
> processing and protection of business partner's personal data are available
> on website:
> https://www.precheza.cz/en/personal-data-protection-principles/
> Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné
> a podléhají tomuto právně závaznému prohlášení o vyloučení odpovědnosti:
> https://www.precheza.cz/01-dovetek/ | This email and any documents
> attached
> to it may be confidential and are subject to the legally binding
> disclaimer:
> https://www.precheza.cz/en/01-disclaimer/
>
> > -Original Message-
> > From: R-help  On Behalf Of pooja sinha
> > Sent: Tuesday, October 5, 2021 2:20 PM
> > To: r-help mailing list 
> > Subject: [R] Need in formatting data for circos plot
> >
> > Hi All,
> >
> > I have gene expression data with differential fold change value and the
> file
> > looks like as below:
> > Chrom start_pos end_pos value
> > 14 20482867 20496901 2.713009346
> > 4 123712710 123718202 -2.20797815
> > 13 80883384 80896042 1.646405782
> > 16 48842551 48844461 -1.636002557
> > 17 28399094 28517527 1.033066311
> > 9 31846044 31913462 -1.738549101
> > 1 45311538 45349706 -1.360867536
> > I wrote a code in R but it is giving error so I need help in trouble
> > shooting:
> > library(circlize)
> > library(gtools)
> > library(dplyr)
> > circos.initializeWithIdeogram(species = "mm10")
> > circos.par("track.height"=0.20)
> >
> > circos.genomicTrackPlotRegion(data = db_tr,ylim = C(-7, 7),
> numeric.column
> > = 4,
> >   panel.fun = function(region,value,...) {
> > cond <- value[,1] < 0.0
> > circos.genomicPoints(region[cond,],
> > value[cond,], pch = ".", cex = 0.1,
> >  col = "khaki4")
> > circos.genomicPoints(region[!cond,],
> > value[!cond,], pch = ".", cex = 0.1,
> >  col = "indianred")
> >   })
> > Error is : Error in C(-7, 7) : object not interpretable as a factor
> >
> > Please help as I am new to circos plot and tried a lot. The file is also
> attached
> > here.
> >
> > Thanks,
> > Puja
> > __
> > R-help@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.
>

[[alternative HTML version deleted]]

__
R-help@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] Need in formatting data for circos plot

[pooja sinha]

Hi All,

I have gene expression data with differential fold change value and the
file looks like as below:
Chrom start_pos end_pos value
14 20482867 20496901 2.713009346
4 123712710 123718202 -2.20797815
13 80883384 80896042 1.646405782
16 48842551 48844461 -1.636002557
17 28399094 28517527 1.033066311
9 31846044 31913462 -1.738549101
1 45311538 45349706 -1.360867536
I wrote a code in R but it is giving error so I need help in trouble
shooting:
library(circlize)
library(gtools)
library(dplyr)
circos.initializeWithIdeogram(species = "mm10")
circos.par("track.height"=0.20)

circos.genomicTrackPlotRegion(data = db_tr,ylim = C(-7, 7), numeric.column
= 4,
  panel.fun = function(region,value,...) {
cond <- value[,1] < 0.0
circos.genomicPoints(region[cond,],
value[cond,], pch = ".", cex = 0.1,
 col = "khaki4")
circos.genomicPoints(region[!cond,],
value[!cond,], pch = ".", cex = 0.1,
 col = "indianred")
  })
Error is : Error in C(-7, 7) : object not interpretable as a factor

Please help as I am new to circos plot and tried a lot. The file is also
attached here.

Thanks,
Puja
__
R-help@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.

Re: [R] Unable to extract gene list from chromosome

[pooja sinha]

Hi David,

That's the only file I have for analysis and I am also getting the final_1
as 0 obs. of  6 variables. My problem is that I am not getting any output.
It seems like I am missing something in the* values* code but I don't know
what. Just for your hint I googled and some people have suggested using
values as vectors which I do not understand. Also when I pick one row of
the start column and do it on the interactive phase it's giving the result
but it's not possible to do one by one due to the large no. of rows. I
posted my problem in biostars but am still waiting for someone to reply.

Thanks,
Puja

On Thu, Apr 8, 2021 at 7:28 PM David Winsemius 
wrote:

>
> On 4/8/21 3:42 PM, pooja sinha wrote:
>
> Hi David,
>
> Sorry I forgot to attach the file. Now it's attached.
>
>
> Now when I go back and check the values of the setup variables after
> seeing an error on the last call,
>
> Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery =
> fullXmlQuery,  :
>   Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: You have an error in your SQL syntax; check the manual that
> corresponds to your MySQL server version for the right syntax to use near
> 'AND (main.seq_region_end_1020 >= '15108600' OR main.seq_region_end_1020 >=
> '9115' at line 1
>
> I now notice:
>
>
> AT_AC_Gene$chr
>
> #NULL
>
> Changing that to AT_AC_Gene$Chromosome_number gets at least a startup
> message from the server:
>
> Batch submitting query
> [==>---]
> 5% eta:  1m
>
> Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery =
> fullXmlQuery,  :
>   Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: You have an error in your SQL syntax; check the manual that
> corresponds to your MySQL server version for the right syntax to use near
> 'AND (main.seq_region_end_1020 >= '15108600' OR main.seq_region_end_1020 >=
> '9115' at line 1
>
> But then I get the same error before about SQL syntax error.
>
>
> Then I ran it with only complete cases and now get no error but again see
> no hits:
>
> str(final_1)
> 'data.frame':0 obs. of  6 variables:
>  $ external_gene_name: logi
>  $ ensembl_gene_id   : logi
>  $ start_position: logi
>  $ end_position  : logi
>  $ rgd_symbol: logi
>  $ chromosome_name   : logi
>
>
> I also see a lot of NA's in that dataset and when I just send the first 10
> rows of the request, I get no error (but also no matches.)
>
>
> So you clearly are not giving us all the data or all the code, but I'm
> finally wondering if you just don't have an data that matches teh external
> datasets in your chosen "biomart". Can you offer a smaller dataset that you
> know with certainty should produce a match?
>
>
> Alternatively, you might want to post this instead at the BioConductor
> mailing list. They are the people who have a better chance of spotting
> obvious errors. I've found two likely code-related errors but I'm not a
> computational biostatistician.
>
> David
>
>
>
> Thanks,
> Puja
>
> On Thu, Apr 8, 2021 at 6:01 PM David Winsemius 
> wrote:
>
>>
>> On 4/8/21 2:30 PM, pooja sinha wrote:
>> > Hi All,
>> >
>> > I am trying to extract gene list from chromosome number and position,
>> for
>> > that I am using biomaRt in R but I am getting error messages as shown
>> > below. Also below is the code I am using for extraction.
>> >
>> > library("biomaRt")
>> > listMarts()
>> > ensembl <- useMart("ensembl")
>> > datasets <- listDatasets(ensembl)
>> > ensembl = useDataset("rnorvegicus_gene_ensembl",mart=ensembl)
>> > AT_AC_Gene <- read.csv("AT-AC-methylkit_biomart-4-7-21.csv",header=T)
>>
>>
>> #--- a this point I get
>>
>> Error in file(file, "rt") : cannot open the connection
>> In addition: Warning message:
>> In file(file, "rt") :
>>cannot open file 'AT-AC-methylkit_biomart-4-7-21.csv': No such file
>> or directory
>>
>> > attributes <-
>> >
>> c("external_gene_name","ensembl_gene_id","start_position","end_position","rgd_symbol","chromosome_name")
>> > filters <- c("chromosome_name","start","end")
>> > values <- list(AT_AC_Gene$chr,AT_AC_Gene$start,AT_AC_Gene$end)
>> > final_1 <- getBM(attributes=attributes, filters=filters, values=values,
>> > mart=ensembl)
>> >

Re: [R] Unable to extract gene list from chromosome

[pooja sinha]

Hi David,

Sorry I forgot to attach the file. Now it's attached.


Thanks,
Puja

On Thu, Apr 8, 2021 at 6:01 PM David Winsemius 
wrote:

>
> On 4/8/21 2:30 PM, pooja sinha wrote:
> > Hi All,
> >
> > I am trying to extract gene list from chromosome number and position, for
> > that I am using biomaRt in R but I am getting error messages as shown
> > below. Also below is the code I am using for extraction.
> >
> > library("biomaRt")
> > listMarts()
> > ensembl <- useMart("ensembl")
> > datasets <- listDatasets(ensembl)
> > ensembl = useDataset("rnorvegicus_gene_ensembl",mart=ensembl)
> > AT_AC_Gene <- read.csv("AT-AC-methylkit_biomart-4-7-21.csv",header=T)
>
>
> #--- a this point I get
>
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>cannot open file 'AT-AC-methylkit_biomart-4-7-21.csv': No such file
> or directory
>
> > attributes <-
> >
> c("external_gene_name","ensembl_gene_id","start_position","end_position","rgd_symbol","chromosome_name")
> > filters <- c("chromosome_name","start","end")
> > values <- list(AT_AC_Gene$chr,AT_AC_Gene$start,AT_AC_Gene$end)
> > final_1 <- getBM(attributes=attributes, filters=filters, values=values,
> > mart=ensembl)
> >
> > The code runs well without any error but the final1 output has 0
> > observations of 6 variables. Why?
> >
> > Can anyone help me with this?
>
>
> You are more likely to get a useful response on the BioC mailing list.
> It appears you have a dependenciy of a csv file that you have not told
> us about.
>
>
> --
>
> David
>
> >
> >
> > Thanks,
> >
> > Puja
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@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@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] Unable to extract gene list from chromosome

[pooja sinha]

Hi All,

I am trying to extract gene list from chromosome number and position, for
that I am using biomaRt in R but I am getting error messages as shown
below. Also below is the code I am using for extraction.

library("biomaRt")
listMarts()
ensembl <- useMart("ensembl")
datasets <- listDatasets(ensembl)
ensembl = useDataset("rnorvegicus_gene_ensembl",mart=ensembl)
AT_AC_Gene <- read.csv("AT-AC-methylkit_biomart-4-7-21.csv",header=T)
attributes <-
c("external_gene_name","ensembl_gene_id","start_position","end_position","rgd_symbol","chromosome_name")
filters <- c("chromosome_name","start","end")
values <- list(AT_AC_Gene$chr,AT_AC_Gene$start,AT_AC_Gene$end)
final_1 <- getBM(attributes=attributes, filters=filters, values=values,
mart=ensembl)

The code runs well without any error but the final1 output has 0
observations of 6 variables. Why?

Can anyone help me with this?


Thanks,

Puja

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] merging multiple .csv files

[pooja sinha]

I know that but I do not want to merge them sequentially because I may lose
some rows which are present in one file while the other doesn't have. I
googled and found something called multmerge but the code is not working
for me. I used the following:

path <-"P:/Documents/Puja Desktop items/Documents/RESULTS/est meth
results/Final_est_meth_data_rn6/WGBS_exon_sort_CHG/merge_csv"


filenames <- list.files(path = path)

View(filenames)
multmerge = function(path){
  filenames=list.files(path=path, full.names=TRUE)
  datalist = lapply(filenames, function(x){read.csv(file=x,header=T)})
  Reduce(function(x,y) {merge(x,y)}, datalist)
}

full_data = multmerge("~/P:/Documents/Puja Desktop
items/Documents/RESULTS/est meth
results/Final_est_meth_data_rn6/WGBS_exon_sort_CHG/merge_csv")

But after running the full_data, the folder is empty.

Thanks,
Puja

On Tue, Dec 15, 2020 at 4:51 PM Bert Gunter  wrote:

> ?read.csv to read your csv files in data frames
> ?merge to merge them (sequentially).
>
>
> 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, Dec 15, 2020 at 1:36 PM pooja sinha  wrote:
>
>> Hi All,
>>
>> I have 10 .csv files containing 12 to 15 columns but have some columns in
>> common. I need to join all of my .csv files into one using one common
>> column ‘Pos’. The header portion of my .csv files looks as shown below:
>>
>> Chrom Pos Avg Stdev  A15_3509.C A31_3799.C A32_3800.C A35_3804.C Gene ID
>> Class ExNum
>>
>>  Can anyone help me in getting the code for the above problem. Any help
>> will be highly appreciated.
>>
>>
>> Thanks,
>>
>> Puja
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@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.
>>
>

[[alternative HTML version deleted]]

__
R-help@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] merging multiple .csv files

[pooja sinha]

Hi All,

I have 10 .csv files containing 12 to 15 columns but have some columns in
common. I need to join all of my .csv files into one using one common
column ‘Pos’. The header portion of my .csv files looks as shown below:

Chrom Pos Avg Stdev  A15_3509.C A31_3799.C A32_3800.C A35_3804.C Gene ID
Class ExNum

 Can anyone help me in getting the code for the above problem. Any help
will be highly appreciated.


Thanks,

Puja

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] Unable to resolve the issue of break point in ggplot2

[pooja sinha]

Sorry I used limits in code and need to focus on both limits and breaks.

On Wed, Feb 26, 2020 at 9:51 AM pooja sinha  wrote:

> Hi All,
>
> I have a data as shown below:
> TF YT_YC MT_MC AT_AC
> GRHL2 1e-2597 1e-2789 1.00E-281
> Srebp1a 1e-1860 1e-1744 1e-944
> EWS:ERG 1e-1831 1e-2127 1e-548
> EWS:FLI1 1e-1580 1e-1937 1.00E-166
> NFAT 1e-1418 1e-2224 1e-761
> Sox4 1e-1410 1e-1839 1.00E-246
> PU.1-IRF 1e-1361 1e-3661 1e-1380
> Sox2 1e-1114 1e-1295 1e-399
> Atoh1 1e-1108 1e-620 1e-590
> EHF 1e-942 1e-1379 1e-1727
> ETV1 1e-927 1e-1301 0.01
> Nur77 1e-908 1e-795 1e-372
> ZNF711 1e-814 1e-684 1e-576
> Sox10 1e-769 1e-1115 1.00E-41
> I am trying to make geom_tile in ggplot2 and I have the code below but
> after plotting I didn't find the gradient of colors after applying breaks.
> Can anyone suggest me how to apply breaks or other codes in ggplot2 so that
> I can have gradient of colors or other way of plotting.
>
> library(ggplot2)
> library(tidyr)
> library(dplyr)
> setwd("C:/Users/sinha.puja/Desktop/CP")
> mat_data1 <-
> read.csv(file="C:/Users/sinha.puja/Desktop/CP/TF_heatmap_plot.csv",
> sep=",")
> library(wesanderson)
> names(wes_palettes)
> pal <- wes_palette("Zissou1", 100, type = "continuous")
> mat_data1 %>%
>   pivot_longer(
> cols = c("YT_YC", "MT_MC", "AT_AC"),
> names_to = "Age_group",
> values_to = "Value"
>   ) %>%
>   ggplot(aes(x = Age_group, y = TF)) +
>   geom_tile(aes(fill=Value), width = 0.990, height = 0.900) +
>   scale_fill_gradientn(colours = pal, limits =c(0.01, 1.e-3670))
>
> Thanks in Advance.
> Puja
>

[[alternative HTML version deleted]]

__
R-help@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] Unable to resolve the issue of break point in ggplot2

[pooja sinha]

Hi All,

I have a data as shown below:
TF YT_YC MT_MC AT_AC
GRHL2 1e-2597 1e-2789 1.00E-281
Srebp1a 1e-1860 1e-1744 1e-944
EWS:ERG 1e-1831 1e-2127 1e-548
EWS:FLI1 1e-1580 1e-1937 1.00E-166
NFAT 1e-1418 1e-2224 1e-761
Sox4 1e-1410 1e-1839 1.00E-246
PU.1-IRF 1e-1361 1e-3661 1e-1380
Sox2 1e-1114 1e-1295 1e-399
Atoh1 1e-1108 1e-620 1e-590
EHF 1e-942 1e-1379 1e-1727
ETV1 1e-927 1e-1301 0.01
Nur77 1e-908 1e-795 1e-372
ZNF711 1e-814 1e-684 1e-576
Sox10 1e-769 1e-1115 1.00E-41
I am trying to make geom_tile in ggplot2 and I have the code below but
after plotting I didn't find the gradient of colors after applying breaks.
Can anyone suggest me how to apply breaks or other codes in ggplot2 so that
I can have gradient of colors or other way of plotting.

library(ggplot2)
library(tidyr)
library(dplyr)
setwd("C:/Users/sinha.puja/Desktop/CP")
mat_data1 <-
read.csv(file="C:/Users/sinha.puja/Desktop/CP/TF_heatmap_plot.csv",
sep=",")
library(wesanderson)
names(wes_palettes)
pal <- wes_palette("Zissou1", 100, type = "continuous")
mat_data1 %>%
  pivot_longer(
cols = c("YT_YC", "MT_MC", "AT_AC"),
names_to = "Age_group",
values_to = "Value"
  ) %>%
  ggplot(aes(x = Age_group, y = TF)) +
  geom_tile(aes(fill=Value), width = 0.990, height = 0.900) +
  scale_fill_gradientn(colours = pal, limits =c(0.01, 1.e-3670))

Thanks in Advance.
Puja

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] Problems in writing code for circos plot

[pooja sinha]

 Hi All,


I had previously mentioned that I have large data set with methylation
values ranging from 0-1. The data contains around 3 million rows of values
corresponding to the chromosomal locations. I want to split/sort my data
for plot using circos plot. I thought of doing like sorting the value range
0.2-0.4 as hypomethylation category and range 0.7-1.0 as hypermethylation
category. However, with this approach the plot again looks cluttered.
Another way is that I can split the data into two parts, one part with
values lower than median, and another part with values larger than median.

Can anyone suggest me which approach is better or if there are other
approaches I can use in my datasets for circos plot using circlize package.


Thanks,

Puja

On Sun, Jan 26, 2020 at 5:06 PM Jim Lemon  wrote:

> Hi Puja,
> Three things:
> 1) Your data files are very large. If you do manage to get circular
> plots out of them with the circlize library they will probably be very
> dense.
> 2) The structure of your data includes too many levels in "Chrom" to
> get the circlize functions to work. I had to pare them back to the
> non-random levels.
> 3) You should probably change the subject line of your message to
> "Would anyone care to do my work for me?"
>
> Jim
>
> On Mon, Jan 27, 2020 at 6:47 AM pooja sinha  wrote:
> >
> > Hi All,
> >
> > I have attached the three different datasets for Rn6 genome (rat) and I
> > needed to use circos plot by *circlize package in R*. Please anyone help
> me
> > in writing the code and making the plot. Any help will be highly
> > appreciated.
> > The three file links are below:
> >
> > File 1: YOUNGCONTROL.csv (
> > https://drive.google.com/open?id=1arQqlzkRJybclikAByB9w9TCnvmD_Y46 )
> > File 2:  YOUNGTREATED.csv (
> > https://drive.google.com/open?id=1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO )
> > File 3:  YOUNGTREATED.vs.YOUNGCONTROL.sig.csv (
> >
> https://drive.google.com/open?id=0B33BGsdd5x_dOGF0X3BuaWRoMmdSYklOZnJoX09uaWdnNEdN
> >  )
> >
> > The circos plot having the outermost ring contain Rn6 ideogram followed
> by
> > YOUNGCONTROL, YOUNGTREATED & last innermost circle will be of
> > YOUNGTREATED.vs.YOUNGCONTROL.sig
> >
> > Thanks,
> > Puja
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@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.
>

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] Unable to make plots using ggplot2

[pooja sinha]

Thanks for your suggestion and code.


Puja

On Sun, Feb 16, 2020 at 5:23 PM Rui Barradas  wrote:

> Hello,
>
> Your error is that you are not plotting the values in your file
> See what is in df, it's one column only with 3 character strings,
> c("Young_Control", "Young_Treated", "CHG_methylation"). Those *are not*
> the names of columns, they are just strings.
>
> The right way of doing it is to reshape your data from wide format to
> long format first. I will reformat with tidyr::pivot_longer and pipe the
> result directly to ggplot.
>
> Also, given the large difference in the values plotted, I suggest you
> comment out the code line with "log10", it will plot the y axis in the
> logarithmic scale.
>
>
> library(tidyverse)
> library(ggplot2)
>
> df1 %>%
>pivot_longer(
>  cols = c("Young_Control", "Young_Treated"),
>  names_to = "Treatment",
>  values_to = "Value"
>) %>%
>ggplot(aes(x = CHG_methylation, y = Value, fill = Treatment)) +
>geom_col(position = position_dodge(0.9)) +
>    #scale_y_continuous(trans = "log10") +
>theme(axis.text.x = element_text(angle = 60, vjust = 1))
>
>
> Hope this helps,
>
> Rui Barradas
>
>
> Às 22:01 de 16/02/20, pooja sinha escreveu:
> > Hi All,
> >
> > I have data in excel with the following details:
> > CHG_methylation Young_Control Young_Treated
> > 0-10% 95.23 94.53
> > 10-20% 3.71 4.16
> > 20-30% 0.68 0.8
> > 30-40% 0.18 0.22
> > 40-50% 0.07 0.09
> > 50-60% 0.04 0.06
> > 60-70% 0.02 0.04
> > 70-80% 0.02 0.03
> > 80-90% 0.02 0.03
> > 90-100% 0.04 0.05
> > I am trying to plot the graph using ggplot2 but not successful yet. My
> code
> > is below:
> >
> > library(readxl)
> > library(dplyr)
> > library(tidyverse)
> > data2 <- read_excel("CHG_meth_plot1.xlsx")
> > df <- data2
> > df <- data.frame(var=c("Young_Control", "Young_Treated",
> "CHG_methylation"))
> > df
> >
> > ggplot(data = df, aes(x = var, y = CHG_methylation)) +
> >geom_bar(aes(fill = CHG_methylation))
> >
> > I am getting error as something is wrong with my df. Also I needed to
> > create breaks in y-axis as I do not know whether it is possible in R or
> > not.
> > Any kind of help is highly appreciated.
> >
> > Thanks,
> > Puja
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@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.
> >
>

[[alternative HTML version deleted]]

__
R-help@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] Unable to make plots using ggplot2

[pooja sinha]

Hi All,

I have data in excel with the following details:
CHG_methylation Young_Control Young_Treated
0-10% 95.23 94.53
10-20% 3.71 4.16
20-30% 0.68 0.8
30-40% 0.18 0.22
40-50% 0.07 0.09
50-60% 0.04 0.06
60-70% 0.02 0.04
70-80% 0.02 0.03
80-90% 0.02 0.03
90-100% 0.04 0.05
I am trying to plot the graph using ggplot2 but not successful yet. My code
is below:

library(readxl)
library(dplyr)
library(tidyverse)
data2 <- read_excel("CHG_meth_plot1.xlsx")
df <- data2
df <- data.frame(var=c("Young_Control", "Young_Treated", "CHG_methylation"))
df

ggplot(data = df, aes(x = var, y = CHG_methylation)) +
  geom_bar(aes(fill = CHG_methylation))

I am getting error as something is wrong with my df. Also I needed to
create breaks in y-axis as I do not know whether it is possible in R or
not.
Any kind of help is highly appreciated.

Thanks,
Puja

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R

[pooja sinha]

Thanks, I'll check it out.

On Fri, Feb 7, 2020 at 1:08 PM Martin Morgan 
wrote:

> Probably have more success asking on https://support.bioconductor.org.
>
> Martin Morgan
>
> On 2/7/20, 12:57 PM, "R-help on behalf of pooja sinha" <
> r-help-boun...@r-project.org on behalf of pjsinh...@gmail.com> wrote:
>
> Hi All,
>
> I have a file list consisting of Chromosome, Start , End & Methylation
> Difference in the following format in excel:
>
> Chrom Start  End  Meth. Diff
>
> chr1 38565900 38566000 -0.20276818
>
> chr1 38870400 38870500 -0.342342342
>
> chr1 39469400 39469500 -0.250260552
>
> chr1 52013600 52013700 -0.37797619
>
> chr1 52751700 52751800  0.257575758
>
> chr1 75505100 75505200 -0.262847308
>
> I need help in plotting the DMRs using Gviz package in R. I tried a
> code
> below but it doesn't turn out correct.
>
> library(GenomicRanges)
> library(grid)
> library(Gviz)
> library(rtracklayer)
> library(BSgenome)
> library(readxl)
> library(BSgenome.Rnorvegicus.UCSC.rn6)
> genome <- getBSgenome("BSgenome.Rnorvegicus.UCSC.rn6")
> genome
> data1 <- read_excel("DMRs_plots.xlsx")
> head(data1)
> data1$Chrom = Chrom$chr1
>
> track1 <- DataTrack(data = data1, from = "38565900" , to = "28225",
> chromosome = Chrom$chr1, name = "DMRs")
>
> itrack <- IdeogramTrack(genome = genome, chromosome = chr)
>
> plotTracks(track1, itrack)
>
>
> If anyone know how to plot and correct my code including how to add
> methylation difference values, then that will be of great help.
>
>
> Thanks,
>
> Puja
>
> [[alternative HTML version deleted]]
>
> __
> R-help@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.
>
>

[[alternative HTML version deleted]]

__
R-help@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] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R

[pooja sinha]

Hi All,

I have a file list consisting of Chromosome, Start , End & Methylation
Difference in the following format in excel:

Chrom Start  End  Meth. Diff

chr1 38565900 38566000 -0.20276818

chr1 38870400 38870500 -0.342342342

chr1 39469400 39469500 -0.250260552

chr1 52013600 52013700 -0.37797619

chr1 52751700 52751800  0.257575758

chr1 75505100 75505200 -0.262847308

I need help in plotting the DMRs using Gviz package in R. I tried a code
below but it doesn't turn out correct.

library(GenomicRanges)
library(grid)
library(Gviz)
library(rtracklayer)
library(BSgenome)
library(readxl)
library(BSgenome.Rnorvegicus.UCSC.rn6)
genome <- getBSgenome("BSgenome.Rnorvegicus.UCSC.rn6")
genome
data1 <- read_excel("DMRs_plots.xlsx")
head(data1)
data1$Chrom = Chrom$chr1

track1 <- DataTrack(data = data1, from = "38565900" , to = "28225",
chromosome = Chrom$chr1, name = "DMRs")

itrack <- IdeogramTrack(genome = genome, chromosome = chr)

plotTracks(track1, itrack)


If anyone know how to plot and correct my code including how to add
methylation difference values, then that will be of great help.


Thanks,

Puja

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] How to extract or sort values from one column

[pooja sinha]

It worked, initially I made some mistake.


Thanks a lot. Trying to read basics of R.

Puja

On Fri, Jan 31, 2020 at 1:06 PM pooja sinha  wrote:

> Thanks but it gives error "incorrect number of dimensions".
>
>
> Best,
> Puja
>
> On Fri, Jan 31, 2020 at 11:37 AM K. Elo  wrote:
>
>> Hi!
>>
>> To extract full rows, use:
>>
>> df[ ( (df$Value>=0.2 & df$Value<=0.4) | df$Value>=0.7 ), ]
>>
>>
>> But it is also a good idea to start reading some introductory
>> tutorials. These are basic things you can find in all tutorials :-)
>>
>> Best,
>> Kimmo
>>
>> pe, 2020-01-31 kello 10:50 -0500, pooja sinha kirjoitti:
>> > Thanks for providing the code but I also needed the output sheet in
>> > .csv format with all the four columns corresponding to the value
>> > (Chrom,
>> > Start_pos, End_pos & Value ranging from what I specified earlier).
>> >
>> > Puja
>> >
>> > On Fri, Jan 31, 2020 at 10:23 AM K. Elo  wrote:
>> >
>> > > Hi!
>> > >
>> > > Oh, sorry, one "s" too much in my code. Here the correct one:
>> > >
>> > > df$Value[ (df$Value>=0.2 & df$Value<=0.4) | df$Value>=0.7 ]
>> > >
>> > > Best,
>> > > Kimmo
>> > >
>> > > pe, 2020-01-31 kello 17:12 +0200, K. Elo kirjoitti:
>> > > > Hi!
>> > > >
>> > > > Let's assume your data is stored in a data frame called 'df'. So
>> > > > this
>> > > > code should do the job:
>> > > >
>> > > > df$Value[ (df$Value>=0.2 & df$Values<=0.4) | df$Value>=0.7 ]
>> > > >
>> > > > Best,
>> > > > Kimmo
>> > > >
>> > > >
>> > > >
>> > > > pe, 2020-01-31 kello 09:21 -0500, pooja sinha kirjoitti:
>> > > > > Hi All,
>> > > > >
>> > > > > I have a .csv file with four columns (Chrom, Start_pos, End_pos
>> > > > > &
>> > > > > Value).
>> > > > > The value column range from 0 to 1.0 having more than 2.8
>> > > > > million
>> > > > > rows. I
>> > > > > need to write a code from which I can extract the values from
>> > > > > 0.2-
>> > > > > 0.4
>> > > > > &
>> > > > > 0.7-1.0. Could anyone help me in writing the code because I am
>> > > > > new
>> > > > > to
>> > > > > R and
>> > > > > it takes lot of time manually to sort based on values.
>> > > > >
>> > > > > The only part I know is I can read the .csv file and after that
>> > > > > I
>> > > > > don’t
>> > > > > know how to proceed further.
>> > > > >
>> > > > >
>> > > > > Thanks,
>> > > > >
>> > > > > Puja
>> > > > >
>> > > > > [[alternative HTML version deleted]]
>> > > > >
>> > > > > __
>> > > > > R-help@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@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@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@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.
>>
>

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] How to extract or sort values from one column

[pooja sinha]

Thanks but it gives error "incorrect number of dimensions".


Best,
Puja

On Fri, Jan 31, 2020 at 11:37 AM K. Elo  wrote:

> Hi!
>
> To extract full rows, use:
>
> df[ ( (df$Value>=0.2 & df$Value<=0.4) | df$Value>=0.7 ), ]
>
>
> But it is also a good idea to start reading some introductory
> tutorials. These are basic things you can find in all tutorials :-)
>
> Best,
> Kimmo
>
> pe, 2020-01-31 kello 10:50 -0500, pooja sinha kirjoitti:
> > Thanks for providing the code but I also needed the output sheet in
> > .csv format with all the four columns corresponding to the value
> > (Chrom,
> > Start_pos, End_pos & Value ranging from what I specified earlier).
> >
> > Puja
> >
> > On Fri, Jan 31, 2020 at 10:23 AM K. Elo  wrote:
> >
> > > Hi!
> > >
> > > Oh, sorry, one "s" too much in my code. Here the correct one:
> > >
> > > df$Value[ (df$Value>=0.2 & df$Value<=0.4) | df$Value>=0.7 ]
> > >
> > > Best,
> > > Kimmo
> > >
> > > pe, 2020-01-31 kello 17:12 +0200, K. Elo kirjoitti:
> > > > Hi!
> > > >
> > > > Let's assume your data is stored in a data frame called 'df'. So
> > > > this
> > > > code should do the job:
> > > >
> > > > df$Value[ (df$Value>=0.2 & df$Values<=0.4) | df$Value>=0.7 ]
> > > >
> > > > Best,
> > > > Kimmo
> > > >
> > > >
> > > >
> > > > pe, 2020-01-31 kello 09:21 -0500, pooja sinha kirjoitti:
> > > > > Hi All,
> > > > >
> > > > > I have a .csv file with four columns (Chrom, Start_pos, End_pos
> > > > > &
> > > > > Value).
> > > > > The value column range from 0 to 1.0 having more than 2.8
> > > > > million
> > > > > rows. I
> > > > > need to write a code from which I can extract the values from
> > > > > 0.2-
> > > > > 0.4
> > > > > &
> > > > > 0.7-1.0. Could anyone help me in writing the code because I am
> > > > > new
> > > > > to
> > > > > R and
> > > > > it takes lot of time manually to sort based on values.
> > > > >
> > > > > The only part I know is I can read the .csv file and after that
> > > > > I
> > > > > don’t
> > > > > know how to proceed further.
> > > > >
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Puja
> > > > >
> > > > > [[alternative HTML version deleted]]
> > > > >
> > > > > __
> > > > > R-help@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@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@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@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.
>

[[alternative HTML version deleted]]

__
R-help@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.

Re: [R] How to extract or sort values from one column

[pooja sinha]

Thanks for providing the code but I also needed the output sheet in
.csv format with all the four columns corresponding to the value (Chrom,
Start_pos, End_pos & Value ranging from what I specified earlier).

Puja

On Fri, Jan 31, 2020 at 10:23 AM K. Elo  wrote:

> Hi!
>
> Oh, sorry, one "s" too much in my code. Here the correct one:
>
> df$Value[ (df$Value>=0.2 & df$Value<=0.4) | df$Value>=0.7 ]
>
> Best,
> Kimmo
>
> pe, 2020-01-31 kello 17:12 +0200, K. Elo kirjoitti:
> > Hi!
> >
> > Let's assume your data is stored in a data frame called 'df'. So this
> > code should do the job:
> >
> > df$Value[ (df$Value>=0.2 & df$Values<=0.4) | df$Value>=0.7 ]
> >
> > Best,
> > Kimmo
> >
> >
> >
> > pe, 2020-01-31 kello 09:21 -0500, pooja sinha kirjoitti:
> > > Hi All,
> > >
> > > I have a .csv file with four columns (Chrom, Start_pos, End_pos &
> > > Value).
> > > The value column range from 0 to 1.0 having more than 2.8 million
> > > rows. I
> > > need to write a code from which I can extract the values from 0.2-
> > > 0.4
> > > &
> > > 0.7-1.0. Could anyone help me in writing the code because I am new
> > > to
> > > R and
> > > it takes lot of time manually to sort based on values.
> > >
> > > The only part I know is I can read the .csv file and after that I
> > > don’t
> > > know how to proceed further.
> > >
> > >
> > > Thanks,
> > >
> > > Puja
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@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@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@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.
>

[[alternative HTML version deleted]]

__
R-help@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] How to extract or sort values from one column

[pooja sinha]

Hi All,

I have a .csv file with four columns (Chrom, Start_pos, End_pos & Value).
The value column range from 0 to 1.0 having more than 2.8 million rows. I
need to write a code from which I can extract the values from 0.2-0.4 &
0.7-1.0. Could anyone help me in writing the code because I am new to R and
it takes lot of time manually to sort based on values.

The only part I know is I can read the .csv file and after that I don’t
know how to proceed further.


Thanks,

Puja

[[alternative HTML version deleted]]

__
R-help@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] Problems in writing code for circos plot

[pooja sinha]

Hi All,

I have attached the three different datasets for Rn6 genome (rat) and I
needed to use circos plot by *circlize package in R*. Please anyone help me
in writing the code and making the plot. Any help will be highly
appreciated.
The three file links are below:

File 1: YOUNGCONTROL.csv (
https://drive.google.com/open?id=1arQqlzkRJybclikAByB9w9TCnvmD_Y46 )
File 2:  YOUNGTREATED.csv (
https://drive.google.com/open?id=1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO )
File 3:  YOUNGTREATED.vs.YOUNGCONTROL.sig.csv (
https://drive.google.com/open?id=0B33BGsdd5x_dOGF0X3BuaWRoMmdSYklOZnJoX09uaWdnNEdN
 )

The circos plot having the outermost ring contain Rn6 ideogram followed by
YOUNGCONTROL, YOUNGTREATED & last innermost circle will be of
YOUNGTREATED.vs.YOUNGCONTROL.sig

Thanks,
Puja

[[alternative HTML version deleted]]

__
R-help@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] Fwd: Problem in plotting Circos plot with the attached dataset

[pooja sinha]

-- Forwarded message -
From: pooja sinha 
Date: Fri 24 Jan, 2020, 15:06
Subject: Problem in plotting Circos plot with the attached dataset
To: 


 YOUNGCONTROL.csv
<https://drive.google.com/file/d/1arQqlzkRJybclikAByB9w9TCnvmD_Y46/view?usp=drive_web>
 YOUNGTREATED.csv
<https://drive.google.com/file/d/1vMidiGmoK4zsYjvf2sT9RbjwF72W0IhO/view?usp=drive_web>
Hi I have attached the three different datasets for Rn6 genome and I needed
to use circos plot by circlize package in R. Please help me in writing the
code and making plot. Any help will be highly appreciated.

The outermost ring contain Rn6 ideogram followed by YOUNGCONTROL,
YOUNGTREATED & last circle will be of
YOUNGTREATED.vs.YOUNGCONTROL.sig

Thanks,
Puja
__
R-help@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] Problem in plotting Circos plot with the attached dataset

[pooja sinha]

 YOUNGCONTROL.csv

 YOUNGTREATED.csv

Hi I have attached the three different datasets for Rn6 genome and I needed
to use circos plot by circlize package in R. Please help me in writing the
code and making plot. Any help will be highly appreciated.

The outermost ring contain Rn6 ideogram followed by YOUNGCONTROL,
YOUNGTREATED & last circle will be of
YOUNGTREATED.vs.YOUNGCONTROL.sig

Thanks,
Puja
__
R-help@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.