[R] How to plot Contour with NA in dataframe
Dear friends,
I am trying to produce Contour Plot with R, but there are some NA
in my data matrix. After I ran the following R script, I got the error
message:no proper `z' matrix specified. Does anybody know how to plot
contour chart with R for the non-strict matrix?
Thank you in advance!!!
myData-read.table('C:/MyDoc/TestData.txt',sep=',')
x - 10*1:nrow(myData)
y - 10*1:ncol(myData)
filled.contour(x, y, myData, color = terrain.colors,
plot.title = title(main = The Topography of Maunga Whau,
xlab = Meters North, ylab = Meters West),
plot.axes = { axis(1, seq(100, 800, by = 100))
axis(2, seq(100, 600, by = 100)) },
key.title = title(main=Height\n(meters)),
key.axes = axis(4, seq(4, 8, by = 1)))
C:/myDoc/TestData.txt is shown as below:
4.95,,5.6250,5.6667,5.90,5.80,5.50,5.70,5.0250,5.90,5.7250,5.75,5.70,5.30,,6,5.50,5.65,,5.7750,5.70,4.90,6.05,,5.4750,5.85,5.55,,,5.8250,5.65,5.75,,5.5750,5.4750,5.3750,5.8750,5.9250,5.55,6.3750,5.70,5.7833,,5.55,
,5.5250,4.856.15,5.8667,,5.20,5.5750,5.74,5.7667,6.7333,6.05,5.8833,5.80,5.8750,,6.15,,5.6250,5.5375,5.65,6,5.8250,5.55,5.85,5.65,5.89,6.15,5.60,,5.65,5.7250,,5.25,6.25,,5.5667,5.9750,6.0250,,,6.35
5.45,,6.30,5.7167,,5.50,6.05,5.8333,5.5833,5.6250,5.70,5.9250,5.7750,6.20,5.5333,5.6625,5.40,5.75,,6,5.5333,,5.6250,5.55,5.65,5.55,5.70,,6.15,5.90,5.7167,6.1167,5.15,6.10,5.4750,,5.75,5.45,5.95,,5.95,5.36676.15,,,
,5.7250,5.75,6,,,5.65,,6.30,5.65,,5.4750,5.60,5.4167,5.8250,,,6.25,6.30,,5.60,6.15,6.10,5.85,,5.8750,5.65,5.9750,5.80,5.65,5.90,6.15,5.5667,5.75,,,6,5.85,5.75,5.7250,5.75
5.75,,6.1167,,5.3250,,5.9167,5.55,,6.05,5.70,5.7250,5.50,6.15,5.40,5.40,5.40,5.70,5.4250,5.7250,5.45,,,5.85,5.85,5.7750,5.8750,5.25,5.45,5.75,5.70,5.65,5.4750,5.7250,5.70,6.10,6.05,5.6875,5.60,,5.80,,,5.65,
5.6250,6.25,5.60,5.90,6.0750,5.80,5.45,5.60,5.50,5.7375,5.60,6,5.9667,5.6833,5.90,5.8333,5.6750,,5.6750,5.7250,5.6833,5.6333,5.65,6.05,,5.57,5.75,5.2750,5.50,,5.6750,5.85,5.6750,6.35,,5.35,
,5.20,,5.5833,5.8333,5.9250,5.7750,5.6667,5.85,5.95,,6.35,5.55,5.3750,,6.30,5.15,5.40,5.55,,5.75,5.45,6.60,,5.45,5.25,,5.25,5.80,5.45,4.80,,5.4250,5.7750,5.15,5.55,5.35,,5.85,5.7667,,,5.60,,
,,,5.15,,6.05,5.4333,5.70,,5.75,6.05,5.15,5.75,5.60,,6.1750,,6.055.5625,5.4167,,5.6250,5.50,5.90,5.95,5.90,6.0250,5.9667,6,5.70,6,5.90,6,5.55,5.8167,5.7750,5.30,,5.77505.40,,,
,6.0667,5.45,5.60,5.55,5.95,5.8750,5.8750,5.80,5.91675.85,5.75,5.5167,,5.8750,,5.45,6.0250,,5.80,5.9375,5.7750,5.5167,,5.8750,5.60,5.8625,5.6333,,5.50,5.2625,5.65,,5.30,5.35,,5.7250,,5.8333,5.85,5.70,,5.30,,,
5.7750,6,5.55,,5.45,5.4125,5.9917,5.50,5.65,5.9750,,,5.7667,5.8333,5.79,5.85,,5.90,5.9833,6.05,,6.3250,6.0750,,5.25,5.85,6.20,,5.45,,,5.65,5.7250,5.9250,6.50,5.35,5.95,,5.8833,5.80,5.95,5.60,5.75,,5.90,6.45,,,
5.6833,5.60,,5.55,5.1250,,6.05,5.75,5.75,5.6833,6,5.55,6.15,5.45,5.70,6.1250,5.67,5.75,5.55,5.35,5.55,5.9750,5.80,5.60,5.9125,5.9375,5.25,5.85,5.4375,6.10,5.55,,,5.6167,5.6167,5.25,6.25,6.1750,5.85,5.5375,5.8250,6.036.10,,,
5.95,5.4667,6.45,5.7375,,5.55,5.6667,5.70,,5.7750,5.50,5.65,5.90,5.8750,5.9750,6,5.6750,,5.8167,,5.50,5.4250,5.65,6,6.1250,5.25,5.90,5.6875,5.6250,,6.2750,6.15,5.7750,5.9250,5.20,5.57,5.92,,5.35,,5.45,5.40,,,
5.65,4.95,5.70,,5.9167,5.3750,5.3750,5.45,5.6167,6.0250,5.8750,5.55,5.85,6.2833,5.9125,5.55,7.85,5.50,6,,5.53,5.35,5.8250,5.75,5.90,5.7167,5.70,5.90,5.4250,5.4750,5.9333,5.95,5.9750,5.45,5.5333,6.2167,5.20,5.10,,5.37,5.7250,5.5167,,,
5.7667,5.65,5.95,,5.95,5.10,5.60,5.70,5.80,5.5625,6.10,5.45,5.5250,,5.6375,6.20,,5.60,5.3750,,5.95,5.5250,5.35,5.70,5.4250,5.75,5.0750,5.60,5.7833,5.50,5.4250,5.85,6.05,5.05,5.7750,,6.20,6.40,5.35,5.6250,5.65,5.755.50,,4.80,
5.9250,5.15,6.0250,5.15,5.40,,6,,,5.8750,,6.10,,5.6750,5.8750,,6.15,6.30,5.80,5.9667,5.95,5.90,5.50,5.8167,5.60,6.0750,5.10,4.95,5.95,5.35,,5.70,6.05,5.7750,5.7250,5.35,5.8250,5.55,5.7667,7.65,5.75,5.8250,,,5.40
Re: [R] How to plot Contour with NA in dataframe
[EMAIL PROTECTED] wrote:
Dear friends,
I am trying to produce Contour Plot with R, but there are some NA
in my data matrix. After I ran the following R script, I got the error
message:no proper `z' matrix specified. Does anybody know how to plot
contour chart with R for the non-strict matrix?
Thank you in advance!!!
myData-read.table('C:/MyDoc/TestData.txt',sep=',')
x - 10*1:nrow(myData)
y - 10*1:ncol(myData)
filled.contour(x, y, myData, color = terrain.colors,
plot.title = title(main = The Topography of Maunga Whau,
xlab = Meters North, ylab = Meters West),
plot.axes = { axis(1, seq(100, 800, by = 100))
axis(2, seq(100, 600, by = 100)) },
key.title = title(main=Height\n(meters)),
key.axes = axis(4, seq(4, 8, by = 1)))
C:/myDoc/TestData.txt is shown as below:
4.95,,5.6250,5.6667,5.90,5.80,5.50,5.70,5.0250,5.90,5.7250,5.75,5.70,5.30,,6,5.50,5.65,,5.7750,5.70,4.90,6.05,,5.4750,5.85,5.55,,,5.8250,5.65,5.75,,5.5750,5.4750,5.3750,5.8750,5.9250,5.55,6.3750,5.70,5.7833,,5.55,
,5.5250,4.856.15,5.8667,,5.20,5.5750,5.74,5.7667,6.7333,6.05,5.8833,5.80,5.8750,,6.15,,5.6250,5.5375,5.65,6,5.8250,5.55,5.85,5.65,5.89,6.15,5.60,,5.65,5.7250,,5.25,6.25,,5.5667,5.9750,6.0250,,,6.35
5.45,,6.30,5.7167,,5.50,6.05,5.8333,5.5833,5.6250,5.70,5.9250,5.7750,6.20,5.5333,5.6625,5.40,5.75,,6,5.5333,,5.6250,5.55,5.65,5.55,5.70,,6.15,5.90,5.7167,6.1167,5.15,6.10,5.4750,,5.75,5.45,5.95,,5.95,5.36676.15,,,
,5.7250,5.75,6,,,5.65,,6.30,5.65,,5.4750,5.60,5.4167,5.8250,,,6.25,6.30,,5.60,6.15,6.10,5.85,,5.8750,5.65,5.9750,5.80,5.65,5.90,6.15,5.5667,5.75,,,6,5.85,5.75,5.7250,5.75
5.75,,6.1167,,5.3250,,5.9167,5.55,,6.05,5.70,5.7250,5.50,6.15,5.40,5.40,5.40,5.70,5.4250,5.7250,5.45,,,5.85,5.85,5.7750,5.8750,5.25,5.45,5.75,5.70,5.65,5.4750,5.7250,5.70,6.10,6.05,5.6875,5.60,,5.80,,,5.65,
5.6250,6.25,5.60,5.90,6.0750,5.80,5.45,5.60,5.50,5.7375,5.60,6,5.9667,5.6833,5.90,5.8333,5.6750,,5.6750,5.7250,5.6833,5.6333,5.65,6.05,,5.57,5.75,5.2750,5.50,,5.6750,5.85,5.6750,6.35,,5.35,
,5.20,,5.5833,5.8333,5.9250,5.7750,5.6667,5.85,5.95,,6.35,5.55,5.3750,,6.30,5.15,5.40,5.55,,5.75,5.45,6.60,,5.45,5.25,,5.25,5.80,5.45,4.80,,5.4250,5.7750,5.15,5.55,5.35,,5.85,5.7667,,,5.60,,
,,,5.15,,6.05,5.4333,5.70,,5.75,6.05,5.15,5.75,5.60,,6.1750,,6.055.5625,5.4167,,5.6250,5.50,5.90,5.95,5.90,6.0250,5.9667,6,5.70,6,5.90,6,5.55,5.8167,5.7750,5.30,,5.77505.40,,,
,6.0667,5.45,5.60,5.55,5.95,5.8750,5.8750,5.80,5.91675.85,5.75,5.5167,,5.8750,,5.45,6.0250,,5.80,5.9375,5.7750,5.5167,,5.8750,5.60,5.8625,5.6333,,5.50,5.2625,5.65,,5.30,5.35,,5.7250,,5.8333,5.85,5.70,,5.30,,,
5.7750,6,5.55,,5.45,5.4125,5.9917,5.50,5.65,5.9750,,,5.7667,5.8333,5.79,5.85,,5.90,5.9833,6.05,,6.3250,6.0750,,5.25,5.85,6.20,,5.45,,,5.65,5.7250,5.9250,6.50,5.35,5.95,,5.8833,5.80,5.95,5.60,5.75,,5.90,6.45,,,
5.6833,5.60,,5.55,5.1250,,6.05,5.75,5.75,5.6833,6,5.55,6.15,5.45,5.70,6.1250,5.67,5.75,5.55,5.35,5.55,5.9750,5.80,5.60,5.9125,5.9375,5.25,5.85,5.4375,6.10,5.55,,,5.6167,5.6167,5.25,6.25,6.1750,5.85,5.5375,5.8250,6.036.10,,,
5.95,5.4667,6.45,5.7375,,5.55,5.6667,5.70,,5.7750,5.50,5.65,5.90,5.8750,5.9750,6,5.6750,,5.8167,,5.50,5.4250,5.65,6,6.1250,5.25,5.90,5.6875,5.6250,,6.2750,6.15,5.7750,5.9250,5.20,5.57,5.92,,5.35,,5.45,5.40,,,
5.65,4.95,5.70,,5.9167,5.3750,5.3750,5.45,5.6167,6.0250,5.8750,5.55,5.85,6.2833,5.9125,5.55,7.85,5.50,6,,5.53,5.35,5.8250,5.75,5.90,5.7167,5.70,5.90,5.4250,5.4750,5.9333,5.95,5.9750,5.45,5.5333,6.2167,5.20,5.10,,5.37,5.7250,5.5167,,,
5.7667,5.65,5.95,,5.95,5.10,5.60,5.70,5.80,5.5625,6.10,5.45,5.5250,,5.6375,6.20,,5.60,5.3750,,5.95,5.5250,5.35,5.70,5.4250,5.75,5.0750,5.60,5.7833,5.50,5.4250,5.85,6.05,5.05,5.7750,,6.20,6.40,5.35,5.6250,5.65,5.755.50,,4.80,
5.9250,5.15,6.0250,5.15,5.40,,6,,,5.8750,,6.10,,5.6750,5.8750,,6.15,6.30,5.80,5.9667,5.95,5.90,5.50,5.8167,5.60,6.0750,5.10,4.95,5.95,5.35,,5.70,6.05,5.7750,5.7250,5.35,5.8250,5.55,5.7667,7.65,5.75,5.8250,,,5.40
Re: [R] How to plot Contour with NA in dataframe
Duncan Murdoch [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Your problem isn't the NA values, it's the fact that the contour
functions want a matrix, and you're passing a data.frame. If you use
as.matrix on it, it converts to character mode, presumably because your
last column is entirely missing (so is read as mode logical, not numeric).
Use this massaging on it and the plot will work:
myData - as.matrix(as.data.frame(lapply(myData,as.numeric)))
This looks unnecessarily complicated here, but appears to be necessary. I
normally would try to use only as.matrix here but this can fail as shown
below, but sometimes can work.
R's rules about this conversion seem somewhat arbitrary to me. Example 3,
in particular, doesn't make sense to me. Can anyone share some insight on
what is going on?
==
Dummy.txt
1,2,3
4,5,6
# 1. Integers, no missing values; as.matrix good enough for conversion
# Results make sense.
myData - read.table('Dummy.txt',sep=',')
typeof(myData)
[1] list
class(myData)
[1] data.frame
myData - as.matrix(myData)
myData
V1 V2 V3
1 1 2 3
2 4 5 6
typeof(myData)
[1] integer
class(myData)
[1] matrix
==
Dummy.txt
1,,3
4,2.5,6
# 2. Doubles, missing values; as.matrix good enough for conversion
# Results make sense.
myData - read.table('Dummy.txt',sep=',')
myData - as.matrix(myData)
myData
V1 V2 V3
1 1 NA 3
2 4 2.5 6
typeof(myData)
[1] double
class(myData)
[1] matrix
==
Dummy.txt
1,,3
# 3. Drop second row of data from 2 above. Now instead of integers or
doubles,
# the type is character after using as.matrix?
# Results don't make sense. Why did dropping the second row of data change
# the type to character here?
myData - read.table('Dummy.txt',sep=',')
myData - as.matrix(myData)
myData
V1 V2 V3
1 1 NA 3
typeof(myData)
[1] character
class(myData)
[1] matrix
==
Dummy.txt
1,,3
# 4. More complicated solution than 3 above, like what Duncan suggested,
# but this gives expected results
myData - read.table('Dummy.txt',sep=',')
myData - as.matrix(as.data.frame(lapply(myData,as.numeric)))
myData
V1 V2 V3
1 1 NA 3
typeof(myData)
[1] double
class(myData)
[1] matrix
==
Thanks for any help in clarifying this R subtilty.
efg
--
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
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