Florian,
I am trying to employ GViz in preparation of figures to accompany a
manuscript in which we characterize the effect a protein knock-down
has on a particular histone modification profile across selected
genes.
I find your vignette very well written and helpful in my aims.
Is it possible to plot multiple bigwigs on a single track, with
distinct colors and alpha blending. I am successfully using the
streaming import on bigwig files to load histone occupancy profiles on
demand. Great!
I would like to be able to overplot two of these bigwigs on a single
track, with distinct colors and alpha blending. is there a backdoor
way of accomplishing this?
You documentation says that passing add=TRUE to plotTracks is needed
to add the plot to existing canvas without re-initializing. I am
writing multiple .png files in an apply, and find that without
add=TRUE the chromosome that I am passing i successive calls is not
being respected. So, in my hands, add=TRUE is required even though
there is no issue of reinitializing or not.
It appears that shape = 'smallArrow' is not respected by
GeneRegionTrack and rect is used regardless.
Finally, are there any ways to annotate tracks further with text,
shaded boxes, horizontal/vertical lines?
Thanks for a very clear vignette with lots of great examples.
~ malcolm_cook at stowers.org / Shilatifard Lab / Compuational Biology
PS Is there a preferred way for hearing issues like this, or is email
to bioc list the best for you?
Hi Malcolm,
good to hear that Gviz is useful for you. See below for more.
On 8/4/13 10:53 AM, "Cook, Malcolm" <mec at="" stowers.org=""> wrote:
>Florian,
>
>I am trying to employ GViz in preparation of figures to accompany a
>manuscript in which we characterize the effect a protein knock-down
has
>on a particular histone modification profile across selected genes.
>
>I find your vignette very well written and helpful in my aims.
>
>Is it possible to plot multiple bigwigs on a single track, with
distinct
>colors and alpha blending. I am successfully using the streaming
import
>on bigwig files to load histone occupancy profiles on demand. Great!
Currently there isn't. What is happening behind the scenes for a
bigwig
file is that the necessary data for the requested genomic region is
extracted and the results are turned into a DataTrack object. From
this
point on, the generic DataTrack plotting method takes over. While
DataTrack objects do support multiple samples as well as the use of
alpha
blending, the problem really is that bigwig files can only contain
data
for a single sample. This is the only reason why we have this one file
<->
one track limitation.
>
>I would like to be able to overplot two of these bigwigs on a single
>track, with distinct colors and alpha blending. is there a backdoor
way
>of accomplishing this?
Of course you could skip the automatic part that streams the bigwig
data
directly into a DataTrack and rebuild this part according to you own
needs. All it takes is wrapper function that takes in the plotting
coordinates and maybe a list of bigwig files that you want to merge.
This
function would than dynamically extract the data from the file, build
a
single DataTrack object containing multiple samples and finally plot
this
object using plotTracks. Obviously this would involve a bit of work
but it
shouldn't be too bad. One thing to keep in mind is that a multi sample
DataTrack can only define a single set of coordinates, which may not
be
the case in your different bigwig files. So you may need to do a bit
of
interpolation, or take the union of all coordinates from all bigwig
files.
>
>You documentation says that passing add=TRUE to plotTracks is needed
to
>add the plot to existing canvas without re-initializing. I am
writing
>multiple .png files in an apply, and find that without add=TRUE the
>chromosome that I am passing i successive calls is not being
respected.
>So, in my hands, add=TRUE is required even though there is no issue
of
>reinitializing or not.
I am afraid I can't follow you on this one. Maybe a short reproducible
code example would help. I assume that you are calling plotTracks in
each
iteration of your apply function, together with the opening and
closing of
a fresh png device. In this case it should't really matter whether you
use
add=true or add=false. The only purpose of this parameter is to skip
calling the grid equivalent of plot.new() before starting the actual
plotting operation. This should have no effect at all on the selected
chromosome. maybe an example will prove me wrong :-)
>
>It appears that shape = 'smallArrow' is not respected by
GeneRegionTrack
>and rect is used regardless.
I can't reproduce this on my end. As a matter of fact, the default
shape
for this class is smallArrow, and I see this respected for instance
when
running the examples from the class' man page. Maybe the strand
information of your object is all '*'? In this cases there will be no
directional informations, alas, no arrows. Or did you set the stacking
to
'dense'? This may also cause the directional information to be lost
when
several elements have to be merged. Again, a reproducible example
would
help.
>
>Finally, are there any ways to annotate tracks further with text,
shaded
>boxes, horizontal/vertical lines?
You can do horizontal lines using the 'baseline' parameter, at least
for
DataTrack objects. All other annotations are currently not supported,
but
very high up on my to do list.
>
>Thanks for a very clear vignette with lots of great examples.
>
>~ malcolm_cook at stowers.org / Shilatifard Lab / Compuational
Biology
>
>
>PS Is there a preferred way for hearing issues like this, or is email
to
>bioc list the best for you?
Florian,
Thanks for the detailed reply.
After a bit more wrangling with both GViz and ggbio I ultimately found
that ggbio was able to meet all my needs.
Again, I found your design and documentation clear and consistent.
It was a pleasure to learn your package and I am likely to use it
again.
Best,
Malcolm
>Hi Malcolm,
>good to hear that Gviz is useful for you. See below for more.
>
>On 8/4/13 10:53 AM, "Cook, Malcolm" <mec at="" stowers.org=""> wrote:
>
>>Florian,
>>
>>I am trying to employ GViz in preparation of figures to accompany a
>>manuscript in which we characterize the effect a protein knock-down
has
>>on a particular histone modification profile across selected genes.
>>
>>I find your vignette very well written and helpful in my aims.
>>
>>Is it possible to plot multiple bigwigs on a single track, with
distinct
>>colors and alpha blending. I am successfully using the streaming
import
>>on bigwig files to load histone occupancy profiles on demand.
Great!
>
>Currently there isn't. What is happening behind the scenes for a
bigwig
>file is that the necessary data for the requested genomic region is
>extracted and the results are turned into a DataTrack object. From
this
>point on, the generic DataTrack plotting method takes over. While
>DataTrack objects do support multiple samples as well as the use of
alpha
>blending, the problem really is that bigwig files can only contain
data
>for a single sample. This is the only reason why we have this one
file <->
>one track limitation.
>
>>
>>I would like to be able to overplot two of these bigwigs on a
single
>>track, with distinct colors and alpha blending. is there a
backdoor way
>>of accomplishing this?
>
>Of course you could skip the automatic part that streams the bigwig
data
>directly into a DataTrack and rebuild this part according to you own
>needs. All it takes is wrapper function that takes in the plotting
>coordinates and maybe a list of bigwig files that you want to merge.
This
>function would than dynamically extract the data from the file,
build a
>single DataTrack object containing multiple samples and finally plot
this
>object using plotTracks. Obviously this would involve a bit of work
but it
>shouldn't be too bad. One thing to keep in mind is that a multi
sample
>DataTrack can only define a single set of coordinates, which may not
be
>the case in your different bigwig files. So you may need to do a bit
of
>interpolation, or take the union of all coordinates from all bigwig
files.
>
>
>>
>>You documentation says that passing add=TRUE to plotTracks is
needed to
>>add the plot to existing canvas without re-initializing. I am
writing
>>multiple .png files in an apply, and find that without add=TRUE the
>>chromosome that I am passing i successive calls is not being
respected.
>>So, in my hands, add=TRUE is required even though there is no issue
of
>>reinitializing or not.
>
>I am afraid I can't follow you on this one. Maybe a short
reproducible
>code example would help. I assume that you are calling plotTracks in
each
>iteration of your apply function, together with the opening and
closing of
>a fresh png device. In this case it should't really matter whether
you use
>add=true or add=false. The only purpose of this parameter is to skip
>calling the grid equivalent of plot.new() before starting the actual
>plotting operation. This should have no effect at all on the
selected
>chromosome. maybe an example will prove me wrong :-)
>
>>
>>It appears that shape = 'smallArrow' is not respected by
GeneRegionTrack
>>and rect is used regardless.
>
>I can't reproduce this on my end. As a matter of fact, the default
shape
>for this class is smallArrow, and I see this respected for instance
when
>running the examples from the class' man page. Maybe the strand
>information of your object is all '*'? In this cases there will be
no
>directional informations, alas, no arrows. Or did you set the
stacking to
>'dense'? This may also cause the directional information to be lost
when
>several elements have to be merged. Again, a reproducible example
would
>help.
>
>>
>>Finally, are there any ways to annotate tracks further with text,
shaded
>>boxes, horizontal/vertical lines?
>
>You can do horizontal lines using the 'baseline' parameter, at least
for
>DataTrack objects. All other annotations are currently not
supported, but
>very high up on my to do list.
>
>>
>>Thanks for a very clear vignette with lots of great examples.
>>
>>~ malcolm_cook at stowers.org / Shilatifard Lab / Compuational
Biology
>>
>>
>>PS Is there a preferred way for hearing issues like this, or is
email to
>>bioc list the best for you?
