R line graphs, values outside plot area

Question

I have 300 variables (columns) taken at 10 timepoints (rows), for each variable at any given timepoint I have temperature values A and F.

Attached is a sample of the dataframe

 structure(list(Timepoint = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 
 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 13L, 13L, 25L, 25L), 
 Temperature = structure(c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 
 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L), .Label = c("A", 
"F"), class = "factor"), Concentration.of.chylomicrons = c(1.29e-11, 
1.25e-11, 1.02e-11, 1.1e-11, 1.08e-11, 1.3e-11, 1.28e-11, 
1.26e-11, 1.06e-11, 1.32e-11, 8.85e-12, 1.21e-11, 8.83e-12, 
1.08e-11, 1.35e-11, 1.12e-11, 8.99e-12, 1.08e-11, 9.55e-12, 
1.04e-11, 0, 1.01e-11), Total.lipids = c(0.00268, 0.0026, 
0.00208, 0.00225, 0.00222, 0.0027, 0.00268, 0.0026, 0.00219, 
0.00273, 0.0018, 0.00247, 0.00179, 0.00221, 0.00276, 0.00229, 
 0.00182, 0.00222, 0.00195, 0.00212, 0, 0.00204), Phospholipids = c(0.000224, 
0.000223, 0.000145, 0.00016, 0.000157, 0.000211, 0.00023, 
0.000211, 0.000165, 0.000224, 0.000109, 0.00018, 0.000113, 
0.000163, 0.000175, 0.000177, 0.000122, 0.000173, 0.000127, 
0.000156, 0, 0.000138)), .Names = c("Timepoint", "Temperature", 
"Concentration.of.chylomicrons", "Total.lipids", "Phospholipids"
), class = "data.frame", row.names = c(NA, -22L))

I would like to draw a line graph to show how each variable varies with time. On this line graph I would like the A and F lines to be drawn.I have successfully managed to write the loop code for this.

# subset based on temperatures A and F
a_df <- subset(df, Temperature == "A")
f_df <- subset(df, Temperature == "F")

# loop from columns 3:x 
for (i in 3:x) {
  plot(a_df[, 1], 
       a_df[, i], 
       type = "l",
       ylab = colnames(a_df[i]),
       xlab = "Timepoint",
       lwd = 2,
       col = "blue")
  lines(f_df[, 1],
        f_df[, i],
        type = "l",
        lwd = 2,
        col = "red")
  legend("bottomleft", 
         col = c("blue", "red"), 
         legend = c("Temperature A", "Temperature F"), 
         lwd = 2,
         y.intersp = 0.5,
         bty = "n")
}

However for certain variables, certain points are outside the plot area, image attached below

Please click on this link for image How can I make sure that in this loop command I can have graghs with all points visible. Im sure there is a quick way to fix this, can anyone help?

I have tried the following line, kindly suggested ylim = c(min(f_df[,-1] ,max(f_df[,-1]),

I get the following error message

for (i in 3:229) { + plot(a_df[, 1], + a_df[, i], + type = "b", + ylim = c(min(f_df[,-1] ,max(f_df[,-1]), + ylab = colnames(f_df[i]), + main = colnames(f_df[i]), + xlab = "Timepoint", + lwd = 2, + col = "red") + lines(f_df[, 1], Error: unexpected symbol in: " col = "red") lines" f_df[, i], Error: unexpected ',' in " f_df[, i]," type = "b", Error: unexpected ',' in " type = "b"," lwd = 2, Error: unexpected ',' in " lwd = 2," col = "blue") Error: unexpected ')' in " col = "blue")" legend("bottomleft", + col = c("red", "blue"), + legend = c("Ambient", "Fridge"), + lwd = 2, + y.intersp = 0.5, + bty = "n") Error in strwidth(legend, units = "user", cex = cex, font = text.font) : plot.new has not been called yet } Error: unexpected '}' in "}"

Lakmal

try ylim = c(min(f_df[,-1] ,max(f_df[,-1]) in your plot command? — dww
Does it matter where in the command I write that line, Im getting the error without any plots — NLM09
would it be an idea to add the plot limits to the plot function in your for loop to match the range of your data? Something like: ylim = c(min(a_df[, i],f_df[, i]),max(a_df[, i],f_df[, i])), edit: same suggestion as dww, but I think you need to specify the range as the min and max in both datasets. You need to put the command in the plot function for it to work. — Niek

Niek Niek · Accepted Answer · 2016-11-30T15:58:18

To recap in an answer. Setting ylim solves the issue

# loop from columns 3:x 
for (i in 3:x) {
  plot(a_df[, 1], 
       a_df[, i], 
       type = "l",
       ylab = colnames(a_df[i]),
       xlab = "Timepoint",
       ylim = c(min(df[,-1]) ,max(df[,-1])),
       lwd = 2,
       col = "blue")
...

sets the plot boundaries as equal for each plot which is better if you want to compare the plots but has the downside that the plot area might be considerably larger than your data.

# loop from columns 3:x 
for (i in 3:x) {
  plot(a_df[, 1], 
       a_df[, i], 
       type = "l",
       ylab = colnames(a_df[i]),
       xlab = "Timepoint",
       ylim = c(min(df[,i]) ,max(df[,i])),
       lwd = 2,
       col = "blue")
...

sets new boundaries for each plot, which is worse for comparison but reduces unnecessary empty plot space. I've replaced min(a_df[, i],f_df[, i])with min(df[,i]) since they should be identical.

R line graphs, values outside plot area

1 Answers