similar to: changing order of lattice plots

Hi, I'm making a multipanel lattice densityplot figure with 2 factors (3 and 20 classes in each factor) with the following statement (the type="percent" is there to prevent plotting the actual points which detract from the figure - is there another way of doing this?): densityplot(~End-Begin | Type * Chromosome, data=Mon, layout=c(5,12), xlab="Element

Dear All, I am trying to build a stacked bar plot, where I define the colours to use. I have asked this before, and I was using a solution in http://thread.gmane.org/gmane.comp.lang.r.general/100649/focus=100673 (thanks, Thierry). However, it looks this works only when the data are in the sequence of the levels in the factor defining the fill colours. When the sequence is different, the

> chromosomes id refseq name length 1 0 NC_000001.9 Homo sapiens chromosome 1 247249719 2 1 NC_000002.10 Homo sapiens chromosome 2 242951149 3 2 NC_000003.10 Homo sapiens chromosome 3 199501827 4 3 NC_000004.10 Homo sapiens chromosome 4 191273063 5 4 NC_000005.8 Homo sapiens chromosome 5 180857866 6 5 NC_000006.10 Homo sapiens chromosome 6

Dear R list, It appears that my request from yesterday got a bit garbled. I have tried to rephrase and retype it - please let me know if you can help me - I am having some trouble drawing a bar-graph with two groups, both of which are stacked. I would like to plot the conservation status according to two classifications (i.e. my groups - IUCN status and national status), and for each of those

Hi, I trying to produce a bar chart describing hits to specific bins by chromosome for a large data set (I am asking here because experimentation with options is precluded due to this - generating the figure takes about an hour): barchart(hits~bin|chromosome, data=hits, horizontal=FALSE, origin=0, lab=c(3,10), layout=c(1,5,5), strip=strip.custom(style=3, bg="grey90",

Dear R list, I am having some trouble drawing a bar-graph with two groups, both of which are stacked. A sample of my data (IUCN and national conservation status for marine and terrestrial species) look like this: Status IUCN Terrestrial IUCN Marine National CS Terrestrial National CS Marine NE 168 69 16 69 LC 41 6 148 6 NT 5 4 7 4 VU 4 2 7 2 EN 4 2 4 2 CR 1

Dear R helpers I would like to be able to colour code the y-axis labels on a complex dot plot by a variable known as company (of which there are only two). The code is below and data attached. Thanks MarkM library("lattice") library(latticeExtra) # for mergedTrellisLegendGrob() # set size of the window windows(height=10, width=7,rescale=c("fixed")) ##read the data to a

Dear all, I have a question about the lattice package, more specifically about the control of the x-axis length in the different panels. I use the following code to make the stacked barchart: barchart(country ~ climatechangefocalpoint + meteorologyservice + adaptationorvulnerability + cdmcarbonmarkets + energy + aviationmaritimetransport + forestry + pressofficer|period, data=graph5,

Hi, Am am plotting aggregated frequency data (extracted from an RDBMS) relating to DNA sequence features for each of the human chromosomes as described in the table chromosomes below (the frequency data is in a table 'hits' that has a value (or not) for each of a set of bins across each chromosome). I would like to mark the extent of the chromosome (according to the length value in

Dear R helpers I would like to move the x-axis labels, which plot automatically at the base of a dot plot to the top of the plot. Is there a way to do this? Code snippet below with(Cal_dat, dotplot(reorder(paste(Mine,Company), Resc_Gt) ~ Resc_Gt, fill_var = Commodity, pch_var = factor(Year), xlab_var = factor(Company), pch = c(21, 22, 23),

Dear all. I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against chromosome and physical location within each chromosome in one plot. The data matrix looks as below: chr location copy_num 1 118345 1.320118 1 3776202 1.133879 1 4798845 0.989997 1 5350951 1.100967 . more data here . . 2 118345 2.459119 2 157739 1.915919 2 1530065 1.924372 2

Dear R-Helpers, I am not very experienced in using lattice and I am still in the learning stage I have a data set which looks like this: (I have deleted a few lines in order to save space) Chromosome marker Marker.Name Distance 1 1 1 PeMm261 0.0000 2 1 2 Xtxp8 10.1013 .. 20 1 20 EbMi148 210.3099 21 1 21 Xtxp25

Hi all, i'm fairly new to R and its graphing, but having unsuccessfully 'googled' and checked this forum to find answer to my problem, i'm posting my question here. I'm trying to plot stacked barplot. I have simple data that looks like this: bg ag 0.41 2.81 0.37 2.91 0.31 2.06 0.32 2.39 every row indicates a factor (1,2,3,4, see below in names.arg). Now when i plot

Dear all, Probably a very basic question but I need some help. I have a data frame (made by read.table from a text file) of microarray data, of which the first column is a factor and the rest of the columns are numeric. The factor column contains chromosome names, so values 1 through 22 plus X, Y and XY. The numeric columns contain positions or intensity measurements. What I need to do is

Hello, I'm writing some genetic simulations in R where I would like to place genes along a chromosome proportional to the density of markers in a given region. For example, a chromosome can be presented as a list of marker locations: Chr1<-c(0, 6.5, 17.5, 26.2, 30.5, 36.4, 44.8, 45.7, 47.8, 48.7, 49.2, 50.9, 52.9, 54.5, 56.5, 58.9, 61.2, 64.1) Where the numbers refer to the locations of

Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, > chromosome <- c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) >barplot (chromosome, col="purple", xlab="Oryza sativa Chromosomes", border = NA, space =

Hello, I have a list with gene names, fold changes (=expression level) and chromosomes. Names fold change chromosome hz 1.5 2 If I plot fold change versus chromosome (or vice versa): plot (ch, fc) I see only the chromosomes with numbers but not those with letter (x and y). What can I do? A second question: How can I add a single line in that plot at a certain

Hello R users, I have a data set which is a set of lengths and types of objects. I want to calculate the mean length for each type of object as opposed to the mean of all the objects in the set. This is in order to make a comparison between the lengths of each type of objects and the number of those objects. > x Chromosome Begin End Type Class Norm Length 458327

My question is twofold. Part 1: My data looks like this: (example set, real data has 2*10^6 rows) binary<-c(1,1,1,0,0,0,1,1,1,0,0) Chromosome<-c(1,1,1,1,1,1,2,2,2,2,2) start<-c(12,17,18,20,25,36,12,15,16,17,19) Table<-cbind(Chromosome,start,binary) Chromosome start binary [1,] 1 12 1 [2,] 1 17 1 [3,] 1 18 1 [4,] 1

Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency.