[BioC] pathview vectorized output?

Luo Weijun luo_weijun at yahoo.com
Mon Jan 20 19:32:44 CET 2014

Thanks for the interest and notes on pathview.
 Please see my responses to your questions below. HTH.

On Sat, 1/18/14, Tobias wrote:

 Subject: pathview vectorized output?

 Date: Saturday, January 18, 2014, 11:52 AM

 Dear Weijun,

 first of all, I would like to congratulate you on this great
 Package. I learned to use it during the last few days and am
 now recommending it to many of my colleagues.

 However, there are some things, I do not understand, or some
 suggestions I'd like to make.

 So far, I only used the fixed KEGG map-layout, so all I
 write about concerns those.

 Do I understand it correctly, that you generate the colored
 overlay from the xml as some kind of vector graphics and
 merge them with the png-files of the KEGG pathways? How do
 you put the EC-numbers for the proteins over them again?
 Would it be possible to have short names of the enzymes
--page 4 of the pathview vignette: 
Graph from the first example above has a single layer. Node colors were modified on the original graph layer, and original KEGG node labels (node names) were kept intact. This way the output file size is as small as the original KEGG PNG file, but the computing time is relative long. If we want a fast view and do not mind doubling the output file size, we may do a two-layer graph with same.layer = F (figure1b). This way node colors and labels are added on an extra layer above the original KEGG graph. Notice that the original KEGG gene labels (or EC numbers) were replaced by official gene symbols.

 Also, if you generate everything as a vector graphic, would
 it also be possible, to generate a completely vectorized
 output in KEGG-Layout? If the connectors are not vectorized:
 one could infer the connection from the reaction the enzyme
 is involved in, and for example, just draw a connector. If
 one is afraid about crossings: if in the end we had an svg
 output, then in inkscape there are nice possibilities to
 just say: 'make connectors not crossing' and it would be a
 nice layout.
--It is not possible to have a vector image in KEGG-Layout because we are limited by the original raster image of KEGG graphs. Remember, these graphs are manually layout and drawn. If you prefer vector images, you may consider the graphviz view (Figure 2,3 etc). These are rendered using the data in xml files. Unfortunately, the metadata on the native KEGG graphs are missing, because these are not part of xml records.

 I also get for some pathways the info, that "none of the
 compounds or genes matched any element in the pathway".
 However, the pngs are still generated, at some dots are also
--This is controlled by map.null argument in pathview function (Default map.null=TRUE).  The argument determines whether to map the NULL gene.data or cpd.data to pathway. Please check the function info for details:

 What I am also looking for is the possibility to change the
 size of the circles, that are drawn for the metabolites. Is
 there any possibility? Where could I find that in the
 package? Your code is relatively readable, however, it would
 be much easier if I just knew where to look for the stuff.
--Currently, we don’t allow users to set the node size, which frequently mess up the output image, e.g. overlapping nodes, unreadable node labels etc. And default node sizes are optimal or necessary. In KEGG view, we intentionally double the size of compound nodes (circles) for better view if you compare pathview graphs with the original ones. 

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