Hi! I am a new R user and have no clue of this error (see below) while using edgeR package: > Y <- clade_reads > y <- Y[,c(g1,g2)] > grouping <- c( rep(1,length(g1)), rep(2,length(g2)) ) > size <- apply(y, 2, sum) > d <- DGEList(data = y, group = grouping, lib.size = size) Error in DGEList(data = y, group = grouping, lib.size = size) : unused argument(s) (data = y) And g1 and g2 are two defined groups. Could anyone kindly interpret this? Many thanks! mikecrux
On 10/15/2010 06:17 AM, Ying Ye wrote:> Hi! > > I am a new R user and have no clue of this error (see below) while using > edgeR package:edgeR is a Bioconductor pacakge so please subscribe to the Bioconductor list and ask there. http://bioconductor.org/help/mailing-list/ include the output of the sessionInfo() command after library(edgeR) Martin> >> Y <- clade_reads >> y <- Y[,c(g1,g2)] >> grouping <- c( rep(1,length(g1)), rep(2,length(g2)) ) >> size <- apply(y, 2, sum) >> d <- DGEList(data = y, group = grouping, lib.size = size) > Error in DGEList(data = y, group = grouping, lib.size = size) : > unused argument(s) (data = y) > > > And g1 and g2 are two defined groups. Could anyone kindly interpret this? > > Many thanks! > > mikecrux > > ______________________________________________ > R-help at r-project.org mailing list > 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.-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
Hi!
I am trying to produce a graph which shows overlap in latitude for a
number of species.
I have a dataframe which looks as follows
species1,species2,species3,species4.....
minlat 6147947,612352,627241,6112791
maxlat 7542842,723423,745329,7634921
I want to produce a graph with one horizontal bar for each species where
minlat sets minimum value and maxlat sets maximum value for the bar. I
want all bars to be stacked on top of eachother to show where I have
overlap.
I have tried using boxplot but it only produces the standard mean and sd
of the two values...
Thanks!
Jonas Josefsson
A) you hijacked another thread. On Oct 15, 2010, at 9:50 AM, Jonas Josefsson wrote:> Hi! > > I am trying to produce a graph which shows overlap in latitude for a > number of species. > > I have a dataframe which looks as follows > > species1,species2,species3,species4..... > minlat 6147947,612352,627241,6112791 > maxlat 7542842,723423,745329,7634921 >B) This "looks" like a data input snafu. It appears that the commas in the original data were not properly specified as delimiters.> > I want to produce a graph with one horizontal bar for each species > where minlat sets minimum value and maxlat sets maximum value for > the bar. I want all bars to be stacked on top of eachother to show > where I have overlap. > > I have tried using boxplot but it only produces the standard mean > and sd of the two values...C) boxplot is designed to handle raw data and then pass plotting responsibility off to the bxp function. Once you address your data input issues you can use bxp. -- David> > Thanks! > > Jonas Josefsson
On 10/16/2010 12:50 AM, Jonas Josefsson wrote:> Hi! > > I am trying to produce a graph which shows overlap in latitude for a > number of species. > > I have a dataframe which looks as follows > > species1,species2,species3,species4..... > minlat 6147947,612352,627241,6112791 > maxlat 7542842,723423,745329,7634921 > > > I want to produce a graph with one horizontal bar for each species where > minlat sets minimum value and maxlat sets maximum value for the bar. I > want all bars to be stacked on top of eachother to show where I have > overlap. > > I have tried using boxplot but it only produces the standard mean and sd > of the two values... >Hi Jonas, I think you want a Gantt chart (see gantt.chart in plotrix) Jim