HI everyone, I'm just starting to get into graphing with R and I need to generate one graph that illustrates the pattern of gene expression for various patients. My data is in .csv format and is as follows and i'm showing below a portion of the data. Pt Coordinate Log2Ratio 1 34046382 -0.023639869 1 34141437 0.016456776 1 34232498 -0.027852121 1 34261900 -0.167065347 2 34364856 -0.182864057 2 34461485 -0.228341688 2 34952694 1.90875531 3 34174705 1.312169128 3 34247833 1.381729262 3 34320273 1.218914649 3 34390545 0.992551194 I can generate the multiple line graphs but i can't get the different colors per patient, nor do i know how to change the pattern of the line. Any ideas and help is greatly appreciated. -- View this message in context: http://r.789695.n4.nabble.com/Multiple-line-graphs-tp3652015p3652015.html Sent from the R help mailing list archive at Nabble.com.
Hi lt2,
I would use the ggplot2 or lattice package. It strikes me as more
effort to do in traditional graphics. Anyway, here are some examples.
Lattice is a very nice package, but I am not quite as familiar with
it, so my examples for it are not representative of its full power.
Cheers,
Josh
####################
# Your data
dat <- read.table(textConnection("
Pt Coordinate Log2Ratio
1 34046382 -0.023639869
1 34141437 0.016456776
1 34232498 -0.027852121
1 34261900 -0.167065347
2 34364856 -0.182864057
2 34461485 -0.228341688
2 34952694 1.90875531
3 34174705 1.312169128
3 34247833 1.381729262
3 34320273 1.218914649
3 34390545 0.992551194"), header = TRUE)
closeAllConnections()
require(ggplot2)
require(lattice)
#### Solution using the ggplot2 package ####
## Using colours by patient
ggplot(dat, aes(x = Coordinate, y = Log2Ratio, colour = factor(Pt))) +
geom_line()
## Mapping Pt to type of line
ggplot(dat, aes(x = Coordinate, y = Log2Ratio)) +
geom_line(aes(linetype = factor(Pt)))
## Nothing, but creating separate plots
ggplot(dat, aes(x = Coordinate, y = Log2Ratio)) +
geom_line() +
facet_grid(Pt ~ .)
#### Solution using the lattice package ####
## Colouring lines
xyplot(Log2Ratio ~ Coordinate, data = dat, group = Pt,
type = "l", auto.key = list(points = FALSE, lines = TRUE))
## Condition on lines
xyplot(Log2Ratio ~ Coordinate | factor(Pt), data = dat, type = "l")
On Thu, Jul 7, 2011 at 9:38 AM, lt2 <lt2 at bcm.edu>
wrote:> HI everyone, I'm just starting to get into graphing with R and I need
to
> generate one graph that illustrates the pattern of gene expression for
> various patients. My data is in .csv format and is as follows and i'm
> showing below a portion of the data.
>
> Pt ? ? ?Coordinate ? ? ?Log2Ratio
> 1 ? ? ? 34046382 ? ? ? ?-0.023639869
> 1 ? ? ? 34141437 ? ? ? ?0.016456776
> 1 ? ? ? 34232498 ? ? ? ?-0.027852121
> 1 ? ? ? 34261900 ? ? ? ?-0.167065347
> 2 ? ? ? 34364856 ? ? ? ?-0.182864057
> 2 ? ? ? 34461485 ? ? ? ?-0.228341688
> 2 ? ? ? 34952694 ? ? ? ?1.90875531
> 3 ? ? ? 34174705 ? ? ? ?1.312169128
> 3 ? ? ? 34247833 ? ? ? ?1.381729262
> 3 ? ? ? 34320273 ? ? ? ?1.218914649
> 3 ? ? ? 34390545 ? ? ? ?0.992551194
>
> I can generate the multiple line graphs but i can't get the different
colors
> per patient, nor do i know how to change the pattern of the line.
>
> Any ideas and help is greatly appreciated.
>
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Multiple-line-graphs-tp3652015p3652015.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.
>
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
https://joshuawiley.com/
Thank you!!!!!
LT
On 7/7/11 3:46 PM, "Joshua Wiley" <jwiley.psych@gmail.com>
wrote:
Hi lt2,
I would use the ggplot2 or lattice package. It strikes me as more
effort to do in traditional graphics. Anyway, here are some examples.
Lattice is a very nice package, but I am not quite as familiar with
it, so my examples for it are not representative of its full power.
Cheers,
Josh
####################
# Your data
dat <- read.table(textConnection("
Pt Coordinate Log2Ratio
1 34046382 -0.023639869
1 34141437 0.016456776
1 34232498 -0.027852121
1 34261900 -0.167065347
2 34364856 -0.182864057
2 34461485 -0.228341688
2 34952694 1.90875531
3 34174705 1.312169128
3 34247833 1.381729262
3 34320273 1.218914649
3 34390545 0.992551194"), header = TRUE)
closeAllConnections()
require(ggplot2)
require(lattice)
#### Solution using the ggplot2 package ####
## Using colours by patient
ggplot(dat, aes(x = Coordinate, y = Log2Ratio, colour = factor(Pt))) +
geom_line()
## Mapping Pt to type of line
ggplot(dat, aes(x = Coordinate, y = Log2Ratio)) +
geom_line(aes(linetype = factor(Pt)))
## Nothing, but creating separate plots
ggplot(dat, aes(x = Coordinate, y = Log2Ratio)) +
geom_line() +
facet_grid(Pt ~ .)
#### Solution using the lattice package ####
## Colouring lines
xyplot(Log2Ratio ~ Coordinate, data = dat, group = Pt,
type = "l", auto.key = list(points = FALSE, lines = TRUE))
## Condition on lines
xyplot(Log2Ratio ~ Coordinate | factor(Pt), data = dat, type = "l")
On Thu, Jul 7, 2011 at 9:38 AM, lt2 <lt2@bcm.edu>
wrote:> HI everyone, I''m just starting to get into graphing with R and I
need to
> generate one graph that illustrates the pattern of gene expression for
> various patients. My data is in .csv format and is as follows and
i''m
> showing below a portion of the data.
>
> Pt Coordinate Log2Ratio
> 1 34046382 -0.023639869
> 1 34141437 0.016456776
> 1 34232498 -0.027852121
> 1 34261900 -0.167065347
> 2 34364856 -0.182864057
> 2 34461485 -0.228341688
> 2 34952694 1.90875531
> 3 34174705 1.312169128
> 3 34247833 1.381729262
> 3 34320273 1.218914649
> 3 34390545 0.992551194
>
> I can generate the multiple line graphs but i can''t get the
different colors
> per patient, nor do i know how to change the pattern of the line.
>
> Any ideas and help is greatly appreciated.
>
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Multiple-line-graphs-tp3652015p3652015.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@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.
>
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
https://joshuawiley.com/
[[alternative HTML version deleted]]