CODEWITHSUNDEEP
rfor-loopplotfill
KKL234
KKL234

Reputation: 367

R shade area under curve loop

I recently asked a question on how to produce multiple plots with 2 y-axes from the same data.frame. The solution works perfectly (available here), however I can't seem to fill in the area under the curve on the second y-axis. "Polygon" seems to be the common solution, but when I try to nest it within my for-loop, I can't figure out how to appropriately select my x and y coordinates. Any suggestions would be useful.

Reproducible sample:

df6 <- structure(list(Year = c("2009", "2009", "2009", "2009", "2009", 
"2009", "2009", "2009", "2009", "2009", "2009", "2009", "2009", 
"2009", "2009", "2009", "2009", "2009", "2009", "2009", "2009", 
"2010", "2010", "2010", "2010", "2010", "2010", "2010", "2010", 
"2010", "2010", "2010", "2010", "2010", "2010", "2010", "2010", 
"2010", "2010", "2010", "2010", "2010", "2010", "2010", "2010", 
"2011", "2011", "2011", "2011", "2011", "2011", "2011", "2011", 
"2011", "2011", "2011", "2011", "2011", "2011", "2011", "2011", 
"2011", "2011", "2011", "2011", "2011", "2011", "2012", "2012", 
"2012"), plot = c("FA6", "FA7", "FK1", "FK2", "FK3", "FO1", "FO2", 
"FO6", "GA2", "GA4", "GR1", "GR2", "HE2", "HE3", "LY1", "LY3", 
"LY8", "NM2", "NM3", "TH3", "TH5", "BR1", "BR8", "FA5", "FA6", 
"FA7", "FK1", "FK2", "FK3", "FO1", "FO2", "FO6", "GA2", "GA4", 
"GR1", "GR2", "HE2", "HE3", "LY1", "LY3", "LY8", "NM2", "NM3", 
"TH3", "TH5", "FA5", "FA6", "FA7", "FK1", "FK2", "FK3", "FO1", 
"FO2", "FO6", "GA2", "GA4", "GR1", "GR2", "HE2", "HE3", "LY1", 
"LY3", "LY8", "NM2", "NM3", "TH3", "TH5", "HE2", "HE3", "TH5"
), AvgRW = c(0.628666666666667, 0.485027777777778, 0.479269230769231, 
0.826875, 0.633269230769231, 1.01830769230769, 1.34580555555556, 
1.13061764705882, 0.422375, 1.377625, 0.535375, 0.366384615384615, 
0.493119047619048, 0.300777777777778, 0.971923076923077, 1.02302941176471, 
1.47245833333333, 1.00654166666667, 0.56425, 1.66342857142857, 
1.28477586206897, 0.860666666666667, 2.10155130769231, 1.74626923076923, 
0.616148148148148, 0.42775, 0.402576923076923, 0.859333333333333, 
0.608961538461538, 1.28303846153846, 1.84344444444444, 1.52214705882353, 
0.425546875, 1.66179166666667, 0.647208333333333, 0.390461538461538, 
0.565892857142857, 0.237388888888889, 1.60419230769231, 1.16611764705882, 
1.95329166666667, 1.18795833333333, 0.655928571428571, 2.009, 
1.36198275862069, 2.61165384615385, 0.873296296296296, 0.596, 
0.485884615384615, 1.13633333333333, 0.684461538461538, 1.30946153846154, 
1.69747222222222, 1.64197058823529, 0.40740625, 1.40716666666667, 
0.641625, 0.428576923076923, 0.729011904761905, 0.376222222222222, 
1.52984615384615, 1.15317647058824, 1.66183333333333, 1.17904166666667, 
0.604857142857143, 1.57425, 1.55772222222222, 0.7315, 0.119, 
1.125875), SampDepth = c(27L, 18L, 13L, 12L, 13L, 13L, 18L, 17L, 
32L, 12L, 12L, 13L, 14L, 18L, 13L, 17L, 12L, 12L, 14L, 14L, 29L, 
21L, 13L, 13L, 27L, 18L, 13L, 12L, 13L, 13L, 18L, 17L, 32L, 12L, 
12L, 13L, 14L, 18L, 13L, 17L, 12L, 12L, 14L, 14L, 29L, 13L, 27L, 
18L, 13L, 12L, 13L, 13L, 18L, 17L, 32L, 12L, 12L, 13L, 14L, 18L, 
13L, 17L, 12L, 12L, 14L, 4L, 9L, 2L, 1L, 8L)), .Names = c("Year", 
"plot", "AvgRW", "SampDepth"), row.names = 2330:2399, class = "data.frame")

Current code (works perfectly without the "xx", "yy", and "polygon" lines):

for (i in df6$plot) {                      #start loop
  png(filename = paste0("C:\\Users\\User\\Desktop\\", i, type="png")) #saves graphs
  par(mar=c(5.1,4.1,4.1,5.1))             #increase right margin
  xx <- c(df6[df6$plot==i, min(df6$Year)], x, df6[df6$plot==i, max(df6$Year)])
  yy <- c(df6[df6$plot==i, min(df6$SampDepth)], y, df6[df6$plot==i, max(df6$SampDepth)])
  polygon(xx, yy, col="gray")
  plot(df6[df6$plot==i,c(1,3)],xaxt="n", type="l", ylab="Avg RW")
  title(main=i,line=2.5)                  #add title
  axis(1,at=as.integer(df6$Year),labels=df6$Year) #bottom axis
  axis(3,at=as.integer(df6$Year),labels=df6$Year) #top axis
  par(new = TRUE)                                 #overlay for secondary y
  plot(df6[df6$plot==i,c(1,4)],xaxt="n",yaxt="n", ylab="",type="l", col="red")
  axis(4)                                         #add secondary y axis
  mtext("Sample Depth", side = 4, line=2)         #add secondary y label
  dev.off()
}

When using this code, I keep getting an error message that my x and y lengths differ.

Upvotes: 0

Views: 192

Answers (1)

Badger
Badger

Reputation: 1053

Your problem originated in the way you were attempting to draw a polygon. Drawing a polygon is actually much simpler than you were trying to make it. Further I subset out the data to work with as it makes it easier to find mistakes (for me). If you want to go back to your in-line subsetting that will be fine as this is just a functional example to show you how to use polygon().

For the colour of the area under the curve I suggest checking out rgb() it allows you to assign an alpha value so as to not wash out the rest of your chart.

Cheers! 

 for (i in df6$plot) {                      #start loop
      ## Cut out the data you are working with
      plotting <- df6[which(df6$plot == i),]

  ## Begin plotting
  png(filename = paste0("C:\\Users\\User\\Desktop\\", i, type="png")) #saves graphs  
  par(mar=c(5.1,4.1,4.1,5.1))             #increase right margin
  plot(plotting[,c(1,3)],xaxt="n", type="l", ylab="Avg RW")

  ## This is what I added
  # This will tell R how to plot the polygon, it need the x values (years) ascending and descending
  # And it needs y values (AvgRW) for the above 0 values as well as the 0 values.
  xx <- c(unique(plotting$Year),rev(unique(plotting$Year)))
  yy <- c(plotting$AvgRW,rep(0,length(unique(plotting$Year))))

  polygon(xx, yy, col="gray")
  title(main=i,line=2.5)                  #add title
  axis(1,at=as.integer(plotting$Year),labels=plotting$Year) #bottom axis
  axis(3,at=as.integer(plotting$Year),labels=plotting$Year) #top axis
  par(new = TRUE)                                 #overlay for secondary y
  plot(plotting[,c(1,4)],xaxt="n",yaxt="n", ylab="",type="l", col="red")
  axis(4)                                         #add secondary y axis
  mtext("Sample Depth", side = 4, line=2)         #add secondary y label
  dev.off()
}

Upvotes: 1

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