I am interested in plotting histograms for the following data
Isoform
Tumor_65_198
Tumor_50_192
Tumor_80_167
Tumor_80_204
Tumor_95_197
Tumor_70_189
Tumor_90_202
Tumor_40_177
Tumor_60_21
Tumor_70_174
Tumor_70_147
Tumor_50_5
ABCC4-2007
1
1
1
6
1
9
10
1
2
0
10
1
ABCC4-2008
5
8
7
5
3
10
5
5
7
3
10
3
ABCC4-2009
0
0
0
0
0
0
0
0
0
0
0
0
ABCC4-2010
0
0
0
0
0
0
0
0
0
0
0
0
ABCC4-2011
0
10
4
3
2
0
2
4
1
4
10
0
ABCC4-2012
0
0
10
0
0
0
0
0
0
0
0
0
ABCC4-2013
7
10
10
10
8
10
10
4
10
0
10
0
ABCG1-0489
1
0
0
1
9
1
6
1
1
0
0
0
ABCG1-0490
0
0
0
0
0
0
0
0
0
0
0
0
ABCG1-0491
2
0
2
3
1
1
2
2
5
2
1
7
Basically 12 different histograms one for each Tumor sample. What is an
easy way to do this?
I was trying to modify the following example code, but I guess I need
some help as I am not very comfortable with R
require(lattice)
sundar.theme <- function() {
par <- col.whitebg()
par$strip.background$col <- rep("#000099", 7)
par$add.text$col <- "#eeeeaa"
par$add.text$font <- 2
par$background$col <- "#ffffff"
par$superpose.line$lty <- rep(1, 7)
par$superpose.line$col[1:2] <- c("#880000",
"#008800")
par$superpose.symbol$col[1:2] <- c("#880000",
"#008800")
par
}
trellis.par.set(sundar.theme())
print( # necessary if the file is source()'d
histogram( ~ height | voice.part, data = singer,
xlab = "Height (inches)", type = "density",
panel = function(x, ...) {
panel.histogram(x, ...)
panel.mathdensity(dmath = dnorm, col = "black",
args = list(mean=mean(x),sd=sd(x)))
} )
)
Thanks ../Murli
[[alternative HTML version deleted]]
Your data seems to have come through messed up but lets assume you have a data frame with one column per tumor. The convert your data to stacked form and call histogram: DF <- data.frame(T1 = 1:10, T2 = 6:15) library(lattice) histogram(~ values | ind, stack(DF)) On 9/1/06, Nair, Murlidharan T <mnair at iusb.edu> wrote:> I am interested in plotting histograms for the following data > > > > Isoform > > Tumor_65_198 > > Tumor_50_192 > > Tumor_80_167 > > Tumor_80_204 > > Tumor_95_197 > > Tumor_70_189 > > Tumor_90_202 > > Tumor_40_177 > > Tumor_60_21 > > Tumor_70_174 > > Tumor_70_147 > > Tumor_50_5 > > ABCC4-2007 > > 1 > > 1 > > 1 > > 6 > > 1 > > 9 > > 10 > > 1 > > 2 > > 0 > > 10 > > 1 > > ABCC4-2008 > > 5 > > 8 > > 7 > > 5 > > 3 > > 10 > > 5 > > 5 > > 7 > > 3 > > 10 > > 3 > > ABCC4-2009 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > ABCC4-2010 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > ABCC4-2011 > > 0 > > 10 > > 4 > > 3 > > 2 > > 0 > > 2 > > 4 > > 1 > > 4 > > 10 > > 0 > > ABCC4-2012 > > 0 > > 0 > > 10 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > ABCC4-2013 > > 7 > > 10 > > 10 > > 10 > > 8 > > 10 > > 10 > > 4 > > 10 > > 0 > > 10 > > 0 > > ABCG1-0489 > > 1 > > 0 > > 0 > > 1 > > 9 > > 1 > > 6 > > 1 > > 1 > > 0 > > 0 > > 0 > > ABCG1-0490 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > ABCG1-0491 > > 2 > > 0 > > 2 > > 3 > > 1 > > 1 > > 2 > > 2 > > 5 > > 2 > > 1 > > 7 > > > > Basically 12 different histograms one for each Tumor sample. What is an > easy way to do this? > > I was trying to modify the following example code, but I guess I need > some help as I am not very comfortable with R > > require(lattice) > > sundar.theme <- function() { > par <- col.whitebg() > par$strip.background$col <- rep("#000099", 7) > par$add.text$col <- "#eeeeaa" > par$add.text$font <- 2 > par$background$col <- "#ffffff" > par$superpose.line$lty <- rep(1, 7) > par$superpose.line$col[1:2] <- c("#880000", "#008800") > par$superpose.symbol$col[1:2] <- c("#880000", "#008800") > par > } > > trellis.par.set(sundar.theme()) > > print( # necessary if the file is source()'d > histogram( ~ height | voice.part, data = singer, > xlab = "Height (inches)", type = "density", > panel = function(x, ...) { > panel.histogram(x, ...) > panel.mathdensity(dmath = dnorm, col = "black", > args = list(mean=mean(x),sd=sd(x))) > } ) > ) > > > > > > > > Thanks ../Murli > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch 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. >
> Your data seems to have come through messed up but lets > assume you have a data frame with one column per tumor. > The convert your data to stacked form and call histogram: > > DF <- data.frame(T1 = 1:10, T2 = 6:15) > > library(lattice) > histogram(~ values | ind, stack(DF))Or with ggplot and reshape: install.packages(ggplot) library(ggplot) qplot(x=value, facets=. ~ variable, data=melt(DF,m=1:2), type="histogram") Hadley
Thanks ../Murli -----Original Message----- From: hadley wickham [mailto:h.wickham at gmail.com] Sent: Friday, September 01, 2006 5:08 PM To: Gabor Grothendieck Cc: Nair, Murlidharan T; r-help at stat.math.ethz.ch Subject: Re: Re: [R] histograms> Your data seems to have come through messed up but lets > assume you have a data frame with one column per tumor. > The convert your data to stacked form and call histogram: > > DF <- data.frame(T1 = 1:10, T2 = 6:15) > > library(lattice) > histogram(~ values | ind, stack(DF))Or with ggplot and reshape: install.packages(ggplot) library(ggplot) qplot(x=value, facets=. ~ variable, data=melt(DF,m=1:2), type="histogram") Hadley