Can someone tell me if there is a way to align plotly plots in R-Markdown?. More specifically: Currently my plots are being placed one after another. I would like to have a grid-like format. I achieved this before, using the simple plot function, but that doesn't seem to work with plotly.
The following is an example of my prior code, that worked with the simple plot function. Can I make that work, assuming I were using plotly?
Thanks in advance.
{r comment = NA,fig.width=14, fig.height=14}
layout(matrix(c(1,2,3,4,5,6,7,8), 4, 2, byrow = TRUE))
m_alt <- miete[miete$baujahr <= 22,]
m_neu <- miete[miete$baujahr > 22,]
plot(table(m_alt$bezirk),main="",ylab="Frequency",xlab="Bezirk")
plot(table(m_neu$bezirk),main="",ylab="Frequency",xlab="Bezirk")
plot(table(m_alt$wohnflaeche),main="",ylab="Frequency",xlab="Wohnfläche")
plot(table(m_neu$wohnflaeche),main="",ylab="Frequency",xlab="Wohnfläche")
plot(table(m_alt$wohnlage,m_alt$zimmerzahl),main="Altbau: Wohnlage u. Zimmerzahl")
plot(table(m_neu$wohnlage,m_neu$zimmerzahl),main="Neubau: Wohnlage u. Zimmerzahl")
plot(table(miete$bezirk,miete$zimmerzahl),main="Bezirk u. Zimmerzahl")
plot(table(miete$warmwasser,miete$bezirk),main="Warmwasser u. Bezirk")
This is the function that is part of FactorMiner package
https://github.com/cran/FactoMineR/blob/master/R/plot.HCPC.R
As an example this is the code I ran
res.pca <- PCA(iris[, -5], scale = TRUE)
hc <- HCPC(res.pca, nb.clust=-1,)
plot.HCPC(hc, choice="3D.map", angle=60)
hc$call$X$clust <- factor(hc$call$X$clust, levels = unique(hc$call$X$clust))
plot(hc, choice="map")
The difference is when i run this hc$call$X$clust <- factor(hc$call$X$clust, levels = unique(hc$call$X$clust))
before plot.HCPC this doesn't change the annotation in the figure but when I do the same thing before I ran this plot(hc, choice="map") it is reflected in the final output.
When i see the plot.HCPC function this is the line of the code that does embed the cluster info into the figure
for(i in 1:nb.clust) leg=c(leg, paste("cluster",levs[i]," ", sep=" "))
legend("topleft", leg, text.col=as.numeric(levels(X$clust)),cex=0.8)
My question I have worked with small function where I understand when i edit or modify which one goes where and does what here in this case its a complicated function at least to me so Im not sure how do I modify that part and get what I would like to see.
I would like to see in case of my 3D dendrogram each of the cluster are labelled with group the way we can do in complexheatmap where we can annotate that are in row or column with a color code so it wont matter what the order in the data-frame we can still identify(it's just visual thing I know but I would like to learn how to modify these)
I am making boxplot by ggplot2, but I want to divide into two groups, treated' and 'control', so I use 'fill=treatment', but still one box in each time point,
however, when I use 'fill=treatment' in barplot, it works,
so can you help me to fix it, really thanks!
newcrk10m <- melt(newcrk10,id.vars="time point",variable.name="treatment",
value.name="value")
ggplot(newcrk10m,aes(`time point`,value,fill=treatment))+
geom_bar(stat="identity",position="dodge")+
scale_x_continuous(breaks = seq(0,72,24))
ggplot(newcrk10m,aes(x=`time point`,y=value,
group=`time point`,fill=treatment))+
geom_boxplot(size=0.5)+scale_x_continuous(breaks = seq(0,72,24))
i fix it, i paste 'time point' and 'treatment' then make a new df, it works, thanks!
I'm producing a plot_gene_map figure by the genoPlotR R package, which gives a horizontal phylogenetic tree where aligned with each leaf is a genomic segment.
Here's a simple example that illustrates my usage and problem:
The plot_gene_map function requires an ade4s' package phylog object which represents the phylogenetic tree:
tree <- ade4::newick2phylog("(((A:0.08,B:0.075):0.028,(C:0.06,D:0.06):0.05):0.0055,E:0.1);")
A list of genoPlotR's dna_seg objects (which are essentially data.frames with specific columns), where the names of the list elements have to match the names of the leaves of tree:
dna.segs.list <- list(A=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.A.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="red")),
B=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.B.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="blue")),
C=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.C.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="green")),
D=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.D.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="yellow")),
E=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.E.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="orange")))
And a list of genoPlotR's annotation objects, which give coordinate information, also named according to the tree leaves:
annotation.list <- lapply(1:5,function(s){
mids <- genoPlotR::middle(dna.segs.list[[s]])
return(genoPlotR::annotation(x1=mids,x2=NA,text=dna.segs.list[[s]]$name,rot=30,col="black"))
})
names(annotation.list) <- names(dna.segs.list)
And the call to the function is:
genoPlotR::plot_gene_map(dna_segs=dna.segs.list,tree=tree,tree_width=2,annotations=annotation.list,annotation_height=1.3,annotation_cex=0.9,scale=F,dna_seg_scale=F)
Which gives:
As you can see the top and right box (gene) names get cut off.
I tried playing with pdf's width and height, when saving the figure to a file, and with the margins through par's mar, but they have no effect.
Any idea how to display this plot without getting the names cut off?
Currently genoPlotR's plot_gene_map does not have a legend option implemented. Any idea how can I add a legend, let's say which shows these colors in squares aside these labels:
data.frame(label = c("A","B","C","D","E"), color = c("red","blue","green","yellow","orange"))
Glad that you like genoPlotR.
There are no real elegant solution to your problem, but here are a few things you can attempt:
- increase annotation_height and reduce annotation_cex
- increase rotation (“rot”) in the annotation function
- use xlims to artificially increase the length of the dna_seg (but that’s a bad hack)
For the rest (including the legend), you’ll have to use grid and its viewports.
A blend of the first 3 solutions:
annotation.list <- lapply(1:5,function(s){
mids <- genoPlotR::middle(dna.segs.list[[s]])
return(genoPlotR::annotation(x1=mids, x2=NA, text=dna.segs.list[[s]]$name,rot=75,col="black"))
})
names(annotation.list) <- names(dna.segs.list)
genoPlotR::plot_gene_map(dna_segs=dna.segs.list,tree=tree,tree_width=2,annotations=annotation.list,annotation_height=5,annotation_cex=0.4,scale=F,dna_seg_scale=F, xlims=rep(list(c(0,110)),5))
For the better solution with grid: (note the "plot_new=FALSE" in the call to plot_gene_map)
# changing rot to 30
annotation.list <- lapply(1:5,function(s){
mids <- genoPlotR::middle(dna.segs.list[[s]])
return(genoPlotR::annotation(x1=mids,x2=NA,text=dna.segs.list[[s]]$name,rot=30,col="black"))
})
names(annotation.list) <- names(dna.segs.list)
# main viewport: two columns, relative widths 1 and 0.3
pushViewport(viewport(layout=grid.layout(1,2, widths=unit(c(1, 0.3), rep("null", 2))), name="overall_vp"))
# viewport with gene_map
pushViewport(viewport(layout.pos.col=1, name="geneMap"))
genoPlotR::plot_gene_map(dna_segs=dna.segs.list,tree=tree,tree_width=2,annotations=annotation.list,annotation_height=3,annotation_cex=0.5,scale=F,dna_seg_scale=F, plot_new=FALSE)
upViewport()
# another viewport for the margin/legend
pushViewport(viewport(layout.pos.col=2, name="legend"))
plotLegend(…)
upViewport()
Hope that helps!
Lionel
Which function or package could I use to add the legend? The R base functions did not seem to work for me. The following message is displayed:
Error in strheight(legend, units = "user", cex = cex) :
plot.new has not been called yet"
t = table(iris$Species)
pie(t, labels=rownames(t))
This draws a simple pie. I want that the labels are a little bit more away from the pie. I checked the par() docu but I think I don't understand it completly and I missed the option for that.
This question is explicite about R's own pie() and not related to any other extern R package.
I don't think you can really do this with the pie function. If you look at View(pie) you'll see that the labels are drawn using the text function. This means that they are not really axis labels, and that par has little effect on them. You could try to do stuff by using the arguments of the text function (i.e. pos = 2, offset = 1) but this will affect all labels in the exact same way and results in warnings. To me it seems that the only way is the stupid way by adding some spaces before/ after labels. ie:
t = table(iris$Species)
nms = rownames(t)
# spaces needed after the labels
nms[2] = paste0(nms[2], strrep(' ', 7))
# spaces needed before the labels
nms[c(1, 3)] = paste0(strrep(' ', 7), nms[c(1, 3)])
pie(t, labels = nms)
If you want to a better solution, you could rewrite the pie function to be a bit more flexible or use a different package.