R help - Dec 2014 - circlize package: different font size for axis labels

Hi, Dr. Gu,
I am trying to highlight some axis labels, for example, "72hL3" as
bold, using the following command:

circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f,
ylim=c(-1.3,1.8),track.height=0.5,panel.fun=function(x,y){circos.axis(major.at=c(2:6),minor.ticks=0,labels=c("L3","72hL3","72hL4","8dF","16dF"),labels.cex=0.8,major.tick.percentage=0.02,h="bottom",
direction="inside", labels.font=c(1,2,1,1,1,1))})Is there a way to do
this using circlize package?
Thanks!

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On Dec 15, 2014, at 8:41 AM, Fix Ace wrote:
> Hi, Dr. Gu,
> I am trying to highlight some axis labels, for example, "72hL3"
as bold, using the following command:
> 
> circos.initialize(factors=female.f, xlim=c(1.8,6.2))
> circos.trackPlotRegion(factors=female.f,
>
ylim=c(-1.3,1.8),track.height=0.5,panel.fun=function(x,y){circos.axis(major.at=c(2:6),minor.ticks=0,labels=c("L3","72hL3","72hL4","8dF","16dF"),labels.cex=0.8,major.tick.percentage=0.02,h="bottom",
> direction="inside", labels.font=c(1,2,1,1,1,1))})
That appears to be the sort of argument names that would suggest the underlying
plot paradigm is base graphics. I would try this as the labels
'argument':

labels=epression("L3", "72hL3", bold(72hL4),
"8dF", "16dF")
> Is there a way to do this using circlize package?
> Thanks!
> 
> 	[[alternative HTML version deleted]]
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> 
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David Winsemius
Alameda, CA, USA

Hi,

In current version, `labels.font` in `circos.axis` can only be a scalar ( a
vector with length one).
But you can first add axes with no labels and then add labels by `circos.text`:

female.f = c("a", "b")
circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f, ylim=c(-1.3,1.8),track.height=0.5,
panel.fun=function(x,y) {
        circos.axis(h = "top", major.at=c(2:6),minor.ticks=0,labels=
rep("", 5),labels.cex=0.8,major.tick.percentage=0.02,
                direction="inside")
        circos.text(2:6, rep(1.5, 5),
c("L3","72hL3","72hL4","8dF","16dF"),
font = c(1, 2, 1, 1, 1), facing = "inside", niceFacing = TRUE)
})

best,
Zuguang
________________________________________
From: Fix Ace [acefix at rocketmail.com]
Sent: 15 December 2014 17:41
To: r-help at r-project.org; Gu, Zuguang
Subject: circlize package: different font size for axis labels

Hi, Dr. Gu,

I am trying to highlight some axis labels, for example, "72hL3" as
bold, using the following command:


circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f,
ylim=c(-1.3,1.8),track.height=0.5,panel.fun=function(x,y){circos.axis(major.at=c(2:6),minor.ticks=0,labels=c("L3","72hL3","72hL4","8dF","16dF"),labels.cex=0.8,major.tick.percentage=0.02,h="bottom",
direction="inside", labels.font=c(1,2,1,1,1,1))})

Is there a way to do this using circlize package?

Thanks!

Hi, Dr. Gu,
Thank you very much for the answer. This trick works.?
Another question, is there a way to change the color or the axis?
Thanks!
 

     On Monday, December 15, 2014 1:39 PM, "Gu, Zuguang" <z.gu at
dkfz-heidelberg.de> wrote:
   

 Hi,

In current version, `labels.font` in `circos.axis` can only be a scalar ( a
vector with length one).
But you can first add axes with no labels and then add labels by `circos.text`:

female.f = c("a", "b")
circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f, ylim=c(-1.3,1.8),track.height=0.5,
panel.fun=function(x,y) {
? ? ? ? circos.axis(h = "top", major.at=c(2:6),minor.ticks=0,labels=
rep("", 5),labels.cex=0.8,major.tick.percentage=0.02,
? ? ? ? ? ? ? ? direction="inside")
? ? ? ? circos.text(2:6, rep(1.5, 5),
c("L3","72hL3","72hL4","8dF","16dF"),
font = c(1, 2, 1, 1, 1), facing = "inside", niceFacing = TRUE)
})

best,
Zuguang
________________________________________

Sent: 15 December 2014 17:41
To: r-help at r-project.org; Gu, Zuguang
Subject: circlize package: different font size for axis labels

Hi, Dr. Gu,

I am trying to highlight some axis labels, for example, "72hL3" as
bold, using the following command:


circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f,
ylim=c(-1.3,1.8),track.height=0.5,panel.fun=function(x,y){circos.axis(major.at=c(2:6),minor.ticks=0,labels=c("L3","72hL3","72hL4","8dF","16dF"),labels.cex=0.8,major.tick.percentage=0.02,h="bottom",
direction="inside", labels.font=c(1,2,1,1,1,1))})

Is there a way to do this using circlize package?

Thanks!

   
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I was trying to ask if there is way to change the color of the axis...
Thanks! 

     On Monday, December 15, 2014 1:39 PM, "Gu, Zuguang" <z.gu at
dkfz-heidelberg.de> wrote:
   

 Hi,

In current version, `labels.font` in `circos.axis` can only be a scalar ( a
vector with length one).
But you can first add axes with no labels and then add labels by `circos.text`:

female.f = c("a", "b")
circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f, ylim=c(-1.3,1.8),track.height=0.5,
panel.fun=function(x,y) {
? ? ? ? circos.axis(h = "top", major.at=c(2:6),minor.ticks=0,labels=
rep("", 5),labels.cex=0.8,major.tick.percentage=0.02,
? ? ? ? ? ? ? ? direction="inside")
? ? ? ? circos.text(2:6, rep(1.5, 5),
c("L3","72hL3","72hL4","8dF","16dF"),
font = c(1, 2, 1, 1, 1), facing = "inside", niceFacing = TRUE)
})

best,
Zuguang
________________________________________

Sent: 15 December 2014 17:41
To: r-help at r-project.org; Gu, Zuguang
Subject: circlize package: different font size for axis labels

Hi, Dr. Gu,

I am trying to highlight some axis labels, for example, "72hL3" as
bold, using the following command:


circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f,
ylim=c(-1.3,1.8),track.height=0.5,panel.fun=function(x,y){circos.axis(major.at=c(2:6),minor.ticks=0,labels=c("L3","72hL3","72hL4","8dF","16dF"),labels.cex=0.8,major.tick.percentage=0.02,h="bottom",
direction="inside", labels.font=c(1,2,1,1,1,1))})

Is there a way to do this using circlize package?

Thanks!

   
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