plot factors with dots in R

Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
 $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x:List of 4
  ..$ : Factor w/ 1 level "0 pmol": 1
  ..$ : Factor w/ 1 level "10 pmol": 1
  ..$ : Factor w/ 1 level "100 pmol": 1
  ..$ : Factor w/ 1 level "1000 pmol": 1
 $ y: num  0.931 1.891 2.24 2.792
plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1
df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
  'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?
Best regards,
Luigi
Hi.
It is probably somewhere in docs, but factors are actually numerics vith
labels. 

So with your original data frame

df$x <- factor(df$x)
plot(as.numeric(df$x), df$y)

gives you points. You need to set labels to x axis though.

Cheers
Petr
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Luigi Marongiu
Sent: Thursday, August 27, 2020 2:16 PM
To: r-help <r-help at r-project.org>
Subject: [R] plot factors with dots in R

Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)

str(df)
'data.frame': 4 obs. of  2 variables:
 $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
 $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x:List of 4
  ..$ : Factor w/ 1 level "0 pmol": 1
  ..$ : Factor w/ 1 level "10 pmol": 1
  ..$ : Factor w/ 1 level "100 pmol": 1
  ..$ : Factor w/ 1 level "1000 pmol": 1
 $ y: num  0.931 1.891 2.24 2.792

plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1

df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
  'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?

--
Best regards,
Luigi

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Thank you, better than before...
Hi.
It is probably somewhere in docs, but factors are actually numerics vith
labels.

So with your original data frame

df$x <- factor(df$x)
plot(as.numeric(df$x), df$y)

gives you points. You need to set labels to x axis though.

Cheers
Petr

-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Luigi Marongiu
Sent: Thursday, August 27, 2020 2:16 PM
To: r-help <r-help at r-project.org>
Subject: [R] plot factors with dots in R

Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)

str(df)
'data.frame': 4 obs. of  2 variables:
 $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
 $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x:List of 4
  ..$ : Factor w/ 1 level "0 pmol": 1
  ..$ : Factor w/ 1 level "10 pmol": 1
  ..$ : Factor w/ 1 level "100 pmol": 1
  ..$ : Factor w/ 1 level "1000 pmol": 1
 $ y: num  0.931 1.891 2.24 2.792

plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1

df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
  'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?

--
Best regards,
Luigi

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.

Best regards,
Luigi
Hello,

The plots that you say give bars (or my equivalent version below) don't 
give bars, what they give are boxplots with just one value and the 
median Q1 and Q3 are all equal.

plot(y ~ factor(x), df, pch = 16)  # boxplot

Is the following what you are looking for?

plot(y ~ as.integer(factor(x)), df, pch = 16, xlab = "x", xaxt = "n")
axis(1, at = as.integer(factor(df$x)), labels = df$x)

Hope this helps,

Rui Barradas

?s 13:16 de 27/08/20, Luigi Marongiu escreveu:
Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)

str(df)
'data.frame': 4 obs. of  2 variables:
  $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
  $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
  $ x:List of 4
   ..$ : Factor w/ 1 level "0 pmol": 1
   ..$ : Factor w/ 1 level "10 pmol": 1
   ..$ : Factor w/ 1 level "100 pmol": 1
   ..$ : Factor w/ 1 level "1000 pmol": 1
  $ y: num  0.931 1.891 2.24 2.792

plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1

df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
   'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?

Hi Luigi,
Maybe just:

plot(as.numeric(factor(x,levels=x)),y,xaxt="n",
 main="Concentration by effect",
 xlab="Concentration",ylab="Effect")
axis(1,at=1:4,labels=x)

Jim

On Thu, Aug 27, 2020 at 10:16 PM Luigi Marongiu
Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)

str(df)
'data.frame': 4 obs. of  2 variables:
 $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
 $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x:List of 4
  ..$ : Factor w/ 1 level "0 pmol": 1
  ..$ : Factor w/ 1 level "10 pmol": 1
  ..$ : Factor w/ 1 level "100 pmol": 1
  ..$ : Factor w/ 1 level "1000 pmol": 1
 $ y: num  0.931 1.891 2.24 2.792

plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1

df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
  'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?

--
Best regards,
Luigi

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)

str(df)
'data.frame': 4 obs. of  2 variables:
 $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
 $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
Perhaps this is a good starting point:

with(df, dotchart(y, labels = x, pch = 16))

-Deepayan
```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x:List of 4
  ..$ : Factor w/ 1 level "0 pmol": 1
  ..$ : Factor w/ 1 level "10 pmol": 1
  ..$ : Factor w/ 1 level "100 pmol": 1
  ..$ : Factor w/ 1 level "1000 pmol": 1
 $ y: num  0.931 1.891 2.24 2.792

plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1

df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
  'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?

--
Best regards,
Luigi

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Thank you, all solutions work!

On Fri, Aug 28, 2020 at 9:02 AM Deepayan Sarkar
On Thu, Aug 27, 2020 at 5:46 PM Luigi Marongiu <marongiu.luigi at gmail.com> wrote:
Hello,
I have a dataframe as follows:
```
x = c("0 pmol", "10 pmol", "100 pmol", "1000 pmol")
y = c(0.9306, 1.8906, 2.2396, 2.7917)
df = data.frame(x, y)

str(df)
'data.frame': 4 obs. of  2 variables:
 $ x: chr  "0 pmol" "10 pmol" "100 pmol" "1000 pmol"
 $ y: num  0.931 1.891 2.24 2.792
```
I would like to visualize the data with the classic dots (pch=16) but:
Perhaps this is a good starting point:

with(df, dotchart(y, labels = x, pch = 16))

-Deepayan

```
plot(df$y ~ df$x)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
which is right because x is not numeric, so I took the factor:
```
plot(df$y ~ factor(df$x)) # gives bars instead of dots
plot(df$y ~ factor(df$x), pch = 16) # this also
```
I tried to convert directly the dataframe:
```
df$x = lapply(df$x, factor)
str(df)
'data.frame': 4 obs. of  2 variables:
 $ x:List of 4
  ..$ : Factor w/ 1 level "0 pmol": 1
  ..$ : Factor w/ 1 level "10 pmol": 1
  ..$ : Factor w/ 1 level "100 pmol": 1
  ..$ : Factor w/ 1 level "1000 pmol": 1
 $ y: num  0.931 1.891 2.24 2.792

plot(r$y ~ r$x, pch = 16)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
```
If I try to pass the number of levels:
```
plot(df$y ~ factor(df$x, 1:4), pch = 16) # this draw a boxplot with
all data on level 1

df$x = lapply(df$x, factor(1:4))
Error in match.fun(FUN) :
  'factor(1:4)' is not a function, character or symbol
```

Since the transformation has given only one level (1), my questions are:
How do I tell R to use a dot instead of a line?
What is the correct way of setting factors?

--
Best regards,
Luigi

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Best regards,
Luigi