R rasterVis levelplot: a white line erroneously appears - r

I am plotting maps of atmospheric pollutant fields, or meteorological field, difference between such fields, often overlayed with orography.
My fields are gridded.
A white line misteriously appears, sometimes two.
This seems to happen a bit randomly. I mean: same code and fields, same line; but when I change fields, or color scales, it changes position, or it disappears, or another one appears. Sometimes horizontal, sometimes vertical.
Here is my code
#!/usr/bin/env Rscript
library(rasterVis)
library(RColorBrewer)
NX <- 468
NY <- 421
hgt <- matrix(0.,NX,NY)
# read from file:
ucon <- file("hgt.dat", open="rb")
for (n in seq(1,NX)) {
hgt[n,] <- readBin(ucon, "numeric", n=NY, size=4)
}
close(ucon)
hgtbks <- c(-100,10,500,1000,1500,2000,2500,3000,3500)
hgtcols <- colorRampPalette(c("gray30","white"))(length(hgtbks)-1)
tit <- "Orography"
bkstart=50.0; bkmax=1500.; bkby=100.
bks <- seq(bkstart, bkmax, bkby)
nbks <- length(bks)
cols <- rev(colorRampPalette(brewer.pal(11,"Spectral"))(nbks-2))
cols <- c("white",cols)
legendbreaks <- seq(1,nbks)
legendlabels <- formatC(bks,digits=3)
legendlabpos <- legendbreaks
rpl <-
levelplot(hgt, margin=FALSE , col.regions= hgtcols, at= hgtbks
, main= list(label=tit, cex=1.8)
, colorkey=list(draw= TRUE, col=cols, at=legendbreaks
, labels=list(labels=legendlabels, at=legendlabpos, cex=1.2))
, xlab=NULL, ylab=NULL, scales= list(draw= FALSE))
png("whiteline.png", width=800, height=840)
plot(rpl)
graphics.off()
I would really like to upload a file with my data, but for the moment
I could not find a way to do it (I don't think I can do it, not even an ASCII file). The data matrix (468x421) is too big to be explicitly included in the code, but it really is the orography file
shown in the picture (elevation in meters above mean sea level).
And here is the resulting "white line" map:
Really, I think this might be a levelplot bug. It seems to happen both when hgt is a matrix and when it is a proper raster object: this doesn't seem to make a difference.
Any idea?

I think I found a workaround.
By setting zero padding on the 4 sides, I managed to make the whiteline disappear from a series of maps.
First I defined:
zpadding <- list(layout.heights= list(top.padding=0, bottom.padding=0),
layout.widths= list(left.padding=0, right.padding=0))
then I added, among the parameters of the levelplot call:
par.settings=zpadding
As I said, I don't think this is a proper solution, but a workaround.
The problem seems related to any rescaling of the plot area.
In fact, when a rescaling is forced by, for example, having 4 or 5 digits (instead of 2 or 3) in the colorbar labels, a white line may reappear.
I hope this may point in the right direction other people, either users or developers of levelplot and related software.

Related

Controlling margins in a genoPlotR plot_gene_map

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"

How to break axis in a barplot (maybe using plotrix gap.barplot)?

I found a lot of SO question and answers addressing break and gaps in axis. But most of them are of low quality (in an SO meaning) because of no example code, no picture or to complex codes. This is why I asking.
I try to use library(plotrix). If there is a solution without it and/or another library it would be ok for me, too.
This is a normal R-barplot.
barplot(c(10,20,500))
To break the axis and add gap I tried this.
gap.barplot(c(10,20,500),gap=c(50,400), col=FALSE)
The result is not beautiful.
There is no space between the bars. space parameter from barplot() is not accepted by gap.barplot().
The bars have different widths.
The position of the tics are not in the middle of the bar.
Can I control that parameters with plotrix? I don't see something about it in the documentation.
Is there another library or solution for my problem?
There are so many different answers because of a lot of individual problems. For your problem you can try the following. But there is always a better solution out there. And IMO its always better to show your complete data instead of cropping it.
# Your data with names
library(plotrix)
d <- c(10,20,500)
names(d) <- letters[1:3]
# Specify a cutoff where the y.axis should be splitted.
co <- 200
# Now cut off this area in your data.
d[d > co] <- d[d > co] - co
# Create new axis label using the pretty() function
newy <- pretty(d)
newy[ newy > co] <- newy[ newy > co] + co
# remove values in your cutoff.
gr <- which(newy != co)
newy <- newy[ gr ]
# plot the data
barplot(d, axes=F)
# add the axis
axis(2, at = pretty(d)[gr], labels = newy)
axis.break(2, co, style = "gap")
As an alternative you can try to log your axis using log="y".

R figure being cropped

Here's a bit of a basic question, you'd think R would automate this always. I'm making a heatmap (basic stuff, png() into heatmap.2() into dev.off()), and my row labels get cleaved off on the right hand side, along with a tiny part of the dendrogram on the left:
Fiddling with the margins manually would eventually lead to a sensible output, but the problem is that this is part of an automated pipeline with biologist users in mind. Surely there's some automated way to do this, right? I mean, in RGui on OSX, a quick reshape of the figure window fixes the layout automatically, so it has to be possible. Thanks, and sorry to bother you.
EDIT: Procedure to reproduce this visualisation:
Input data:
Time,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48
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CATMA3A21390,-0.54603,-0.32262,-0.29966,-0.22463,-0.49654,-1.0552,-1.0705,-0.93928,-0.71247,-2.7228,-0.67849,-0.24868,-1.5015,-0.22486,-0.26215,-0.34298,-0.73168,-0.33699,-0.3455,-0.5349,-0.68784,-0.47506,-1.2541,0.86942,-0.14503,-2.0603,-0.35647,-0.67731,0.20243,-1.1881,-1.3828,-1.0471,-0.20157,-2.5492,-0.7862,-0.21715,-0.20583,-0.067758,-0.86589,-0.75509,-0.62777,-0.57176,-2.0996,-0.72894,-0.56391,-1.1054,-0.94172,-0.98805,-0.20763,-0.42764,-2.0142,-1.4079,-0.66326,-0.10354,-1.6284,-1.9413,-0.77001,-0.58492,-0.99846,-0.013285,-0.31205,-0.10665,-1.2396,-1.7556,-0.40454,-0.26631,-1.2694,-0.32263,-1.2293,-0.93683,0.97994,-1.8696,-0.26859,-0.25661,-0.33193,-0.83889,-0.25944,-0.63826,0.3387,-1.4443,-0.93123,-0.84915,-0.24606,-0.63109,-0.78621,-0.40802,-0.6463,-0.84319,-1.0379,-1.1471,1.9932,-1.3029,1.5286,-0.19754,0.018446,-0.55479
CATMA3A53880,3.917,3.6689,3.7213,3.8812,3.8253,4.4861,4.258,4.7926,4.9737,4.0869,3.2183,3.5812,3.408,3.3128,3.3915,4.1923,3.9122,4.0586,4.2707,4.3077,4.8926,4.1982,3.4817,3.5267,3.6952,3.6632,3.9304,4.0793,3.9499,4.2175,4.8303,4.9599,4.6336,3.8998,3.7932,3.8572,3.2167,3.7749,4.3971,4.0662,3.9241,4.6407,4.2837,4.9644,4.972,4.2565,3.8796,3.383,3.2382,4.1017,4.058,4.0423,3.6033,4.0774,5.141,4.9736,4.4372,3.8969,3.7386,3.3618,3.539,4.2588,3.4726,3.7424,3.5818,4.9159,4.3567,4.1291,4.1108,4.4035,3.1374,3.4675,3.762,3.9264,3.7319,4.1205,2.0915,4.4192,4.5049,4.5427,4.6205,3.4653,3.6017,3.3376,3.266,3.5561,3.4538,3.761,4.2013,4.1787,4.017,4.7773,3.748,4.4977,3.8685,3.7464
CATMA5A09500,6.2838,5.1076,6.6209,5.7153,5.9395,5.3601,4.2366,5.189,3.3074,4.8701,5.0357,5.0951,6.2843,5.691,5.5054,5.9949,5.0834,5.1484,4.5884,4.805,4.458,5.0816,4.7264,5.3661,5.0645,5.8293,5.2877,5.6602,5.3336,4.7329,4.843,5.1901,3.8431,4.683,5.7106,4.0774,6.5689,5.8061,5.3445,5.2905,3.837,4.6271,4.2277,4.6165,4.0081,4.5176,4.259,4.6363,4.8557,3.9828,5.9728,5.4698,5.4102,4.5802,5.0247,4.8967,4.0116,2.6636,5.4684,4.3454,6.6893,6.5624,6.1464,5.4444,5.3309,5.6682,5.5012,4.3162,2.9028,3.3906,4.6684,4.914,5.3601,5.5138,6.2191,5.8043,5.8165,5.1155,3.8681,4.9268,4.0232,6.1699,4.6327,5.7364,6.1934,6.7188,5.0755,5.7058,5.3703,4.3921,3.2108,4.9503,4.1003,4.8225,4.6701,4.7166
CATMA5A12680,1.7891,1.362,1.4303,0.61973,0.54124,1.2733,0.7775,0.66788,1.7338,0.63125,1.5852,0.91616,1.0712,0.81919,0.90152,0.77799,1.0835,0.32735,2.0868,0.5895,1.1445,0.64545,0.71776,0.33929,1.42,1.0729,1.4879,0.86379,0.95453,1.2928,0.97753,1.1738,0.79397,0.31563,0.86345,0.67595,1.3501,1.079,1.2034,1.2432,1.3696,1.1473,0.72528,0.57199,0.85965,0.65339,0.47614,0.43219,1.363,2.4026,0.98947,0.85204,1.2591,2.3151,1.6775,1.6555,1.0371,2.5586,-0.097071,0.91744,1.068,1.6819,1.0122,0.99911,0.75267,1.2195,0.42175,0.2554,0.4819,0.80025,0.44517,0.32442,1.9863,1.5019,1.2893,1.0669,1.6881,1.7581,1.6505,1.943,2.141,1.018,0.68207,0.84392,1.1452,1.009,1.1376,1.0572,1.9258,1.7039,0.10261,1.4549,0.94693,0.77945,0.049658,0.84178
CATMA5A14990,0.41247,0.51378,0.375,-0.24526,0.027658,-0.015345,-0.028278,-0.2643,0.3905,0.12299,0.94334,0.11482,0.50109,-0.55162,0.10768,-0.26433,-0.31064,-0.76526,1.0147,-0.73178,0.3323,-0.13657,-0.14013,-0.17878,0.31259,0.36723,0.55499,-0.2664,0.31862,0.60225,0.078919,0.18282,0.23014,-0.27835,0.16392,0.58131,1.052,0.062394,0.064929,-0.11918,-0.2167,-0.26018,-0.21649,-0.032523,-0.05763,-0.62775,-0.29148,0.13633,0.72715,1.535,0.08501,0.76137,0.54934,1.5163,-0.26612,0.58127,0.30339,1.8464,-0.17161,0.30309,-0.070279,0.28016,-0.036628,0.67464,0.34753,0.26499,-0.17856,-0.61162,-0.17941,-0.01017,0.21112,0.026389,0.64566,-0.39685,0.31403,-0.21637,1.1253,0.41434,0.77759,0.20421,0.70657,0.53273,-0.67276,-0.65656,0.6997,-0.06428,-0.13546,-0.15055,0.99804,1.4673,-0.47155,-0.056436,0.84609,-0.23068,-0.55114,0.68975
CATMA5A25890,-0.23072,0.82252,0.32512,0.13284,0.14406,0.005071,0.40953,-0.11252,-0.6367,-0.048073,0.21325,-0.046316,-0.35078,1.1023,-0.019882,-0.55825,-0.34621,0.1114,0.030302,-0.08142,0.19157,0.5152,-0.034952,0.20984,1.0547,0.4816,0.31078,0.14731,0.31811,-0.27275,-0.47217,-0.043207,0.29109,0.41192,-1.069,0.23357,-0.17453,0.015661,-0.26869,0.14587,0.19336,0.5926,-0.1583,0.61242,0.18635,0.01207,-0.21772,0.13986,1.9305,0.3349,0.62954,-0.04455,1.121,-0.14155,-0.33772,-0.42633,0.41828,-0.29794,-0.7107,1.4786,-0.37442,-0.45371,0.16175,-0.057764,-0.11803,-0.037838,0.25868,0.88605,0.33225,-0.24331,0.93084,-0.33266,0.9762,0.24755,0.30857,0.14661,1.8351,0.40313,0.45084,-0.52105,-0.31271,-0.37122,-0.28615,-0.0023692,-0.43072,-0.24417,-0.5184,0.13874,-0.32606,-0.1705,2.1396,-0.77657,2.3056,0.32096,0.29337,-0.034746
CATMA5A31940,4.4307,4.8735,4.7911,5.8201,5.9587,5.576,5.9084,5.849,5.2832,5.5423,5.0275,4.5254,4.5054,3.0696,5.6512,4.3986,4.9856,4.9222,4.951,4.5506,4.2185,4.3184,5.4783,4.4515,3.9397,5.6269,5.0988,6.1254,5.7446,5.6146,5.452,5.2047,5.3527,5.93,4.8931,5.5529,3.9876,4.1072,4.0583,5.4324,5.4681,4.392,4.5189,5.0629,4.9347,5.2165,4.6681,4.7428,4.1539,6.3376,5.353,6.2896,5.5844,5.1654,5.4391,5.3933,5.261,5.6974,4.5142,3.9851,3.569,4.0946,4.6662,5.1085,5.0319,4.4598,4.8672,3.7326,5.3032,5.0448,4.7771,4.2209,4.1886,4.284,5.4681,5.8331,4.7683,5.6614,5.3313,5.2017,5.1002,5.0642,4.4867,4.8576,4.1454,4.0971,5.0368,4.845,4.753,5.5496,2.9838,5.1394,3.342,4.1246,5.0121,4.618
Code proper (BHC is from Bioconductor):
library(argparse)
library(RColorBrewer)
library(BHC)
library(parallel)
library(gplots)
#data prep and clustering, to get dendrograms etc as shown in plot
data = read.csv('input.csv',header=TRUE,row.names=1,check.names=FALSE)
genes = rownames(data)
samples = colnames(data)
data = data.matrix(data)
standardisedData = (data-mean(data))/sd(data)
samples = as.numeric(samples)
hc = bhc(standardisedData, genes, timePoints=samples, dataType='time-course', verbose=TRUE)
#the plotting proper
png('heatmap.png',width=6,height=6,units='in',res=300)
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'))
#heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(3,10)) <- this fixes it on a single-case basis
dev.off()
I would suggest just giving it a fairly wide default margin, such that it should be clipped even with longer labels, e.g.:
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(14, 14))
The default margin size is (5,5). The above increases the both the column and row margins, but you can increase just one or the other as well.
If you want to be more precise, you could try using max(strwidth(rownames(standardisedData))) to determine the amount of space needed by the largest label, and then convert that into the units expected by par(mar=*) (what heatmap.2() uses to specify plot margins.)
I think this should do the trick:
# determine margins to use
png('/tmp/trash', width=6,height=6,units='in',res=300)
plot.new()
margin_width = max(strwidth(rownames(standardisedData), units='inches')) * par('fin')[1]
dev.off()
#the plotting proper
png('heatmap.png',width=6,height=6,units='in',res=300)
heatmap.2(standardisedData, Colv=NA, Rowv=hc, tracecol=NA, scale="none", col=brewer.pal(11,'RdBu'), margins=c(5, margin_width))
dev.off()

ggplot Multiline Title with Different Font Sizes

<SlightlyLookingAway>I am attempting to reproduce an excel plot in R.</SlightlyLookingAway> The Excel plot has a two line title. I know how to handle this by putting a '\n' in the title text. What I do not know how to handle is that the first line has a larger font size than the second row of the title... I have done some google searching and have come up with a general lack of response.
I realize that I might be able to cobble something together with an annotation of some kind but that seemed like a kludge. If that is the only answer then it is, but I wanted to ask the community first.
Any ideas?
It looks as though I have found a hacked solution which gets the job done but does not offer a lot of flexability. The idea is to put in a math expression using the atop() command along with the bold() and scriptstyle() functions.
myplot +
ggtitle(expression(atop(bold("This is the Top Line"), scriptstyle("This is the second line")))) +
theme(plot.title = element_text(size = 20))
If you know of a better solution with more control over the line spacing and even being able to adjust the font face, please let me know...
try this,
library(gridExtra)
titleGrob <- function(x=c("First line", "second line"), size=10, ...){
n <- length(x)
size <- rep(size, length.out=n)
one_label <- function(x, size, ...)
textGrob(x, gp=gpar(fontsize=size), ...)
lg <- mapply(one_label, x=x, size=size, ..., SIMPLIFY=FALSE)
wg <- lapply(lg, grobWidth)
hg <- lapply(lg, grobHeight)
widths <- do.call(unit.c, wg)
heights <- do.call(unit.c, hg)
maxwidth <- max(widths)
g <- frameGrob(layout = grid.layout(n, 1, width=maxwidth, height=heights) )
for(ii in seq_along(lg))
g <- placeGrob(g, lg[[ii]], row=ii)
g
}
grid.newpage()
g <- titleGrob(size=c(18,12))
grid.arrange(qplot(1,1), top=g)
To perfectly center everything (which \n will not do), adapt every size of text whatever the number of lines and at the same time being able to adjust the interlinear space, use this instead:
e.g. for smaller to larger text size
ggtitle(expression(atop(scriptscriptstyle("whateverline1"),atop(scriptstyle("whateverline2"),atop(scriptscriptstyle(""),textstyle("whateverline3"))))))
Then use labeller=label_parsed
This also works for facet_grid, xlab and ylab
Note the scriptscriptstyle("") to control spacing between lines. You can also use varied relative sizes of text using scriptstyle or scriptscriptstyle or textstyle depending on your needs and of course use element_text(size=whatevernumber) in the theme section

Clearing plotted points in R

I am trying to use the animation package to generate an "evolving" plot of points on a map. The map is generated from shapefiles (from the readShapeSpatial/readShapeLines functions).
The problem is when it's plotted in a for loop, the result is additive, whereas the ideal result is to have it evolve.
Are there ways of using par() that I am missing?
My question is: is there a way to clear just the points ploted from the points function
and not clearing the entire figure thus not having to regraph the shapefiles?
in case someone wants to see code:
# plotting underlying map
newyork <- readShapeSpatial('nycpolygon.shp')
routes <- readShapeLines('nyc.shp')
par(bg="grey25")
plot(newyork, lwd=2, col ="lightgray")
plot(routes,add=TRUE,lwd=0.1,col="lightslategrey")
# plotting points and save to GIF
ani.options(interval=.05)
saveGIF({
par(bg="grey25")
# Begin loop
for (i in 13:44){
infile <-paste("Week",i,".csv",sep='')
mydata <-read.csv(file = infile, header = TRUE, sep=",")
plotvar <- Var$Para
nclr <- 4
plotclr <-brewer.pal(nclr,"RdPu")
class<- classIntervals(plotvar,nclr,style = "pretty")
colcode <- findColours(class,plotclr)
points(Var$Lon,Var$Lat,col=colcode)
}
})
If you can accept a residual shadow or halo of ink, you can over-plot with color ="white" or == to your background choices. We cannot access your shape file but you can try it out by adding this line:
points(Var$Lon, Var$Lat, col="grey25")
It may leave gaps in other previously plotted figures or boundaries, because it's definitely not object-oriented. The lattice and ggplot2 graphics models are more object oriented, so if you want to post a reproducible example, that might be an alternate path to "moving" forward. I seem to remember that the rgl package has animation options in its repetoire.

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