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... On Thu, Aug 27, 2020 at 2:37 PM PIKAL Petr <petr.pikal at precheza.cz> wrote:> > 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 <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: > ``` > > 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.
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.
Thank you, all solutions work! On Fri, Aug 28, 2020 at 9:02 AM Deepayan Sarkar <deepayan.sarkar at gmail.com> wrote:> > 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