visreg: overlay two models in a single plot










0














I'm trying to draw in a single plot crude and adjusted GAM models using library visreg:



# Create DF
set.seed(123)
x1 = rnorm(2000)
z = 1 + 3*x1 + 3*exp(x1)
pr = 1/(1+exp(-z))
y = rbinom(2000,1,pr)
df = data.frame(y=y,x1=x1, x2=exp(x1)*z)

# Fitting GAMs
library(mgcv)
crude <- gam(y ~ s(x1), family=binomial(link=logit), data=df)
adj <- gam(y ~ s(x1) + s(x2), family=binomial(link=logit), data=df)

# Plot results using 'visreg'
library(visreg)
p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), gg=TRUE) + theme_bw()
p.adj <- visreg(adj, scale='response', "x1", gg=TRUE) + theme_bw()


Using gridExtra I can produce a two columns plot, however I would have a single plot which overlays the two model plots.



enter image description here










share|improve this question


























    0














    I'm trying to draw in a single plot crude and adjusted GAM models using library visreg:



    # Create DF
    set.seed(123)
    x1 = rnorm(2000)
    z = 1 + 3*x1 + 3*exp(x1)
    pr = 1/(1+exp(-z))
    y = rbinom(2000,1,pr)
    df = data.frame(y=y,x1=x1, x2=exp(x1)*z)

    # Fitting GAMs
    library(mgcv)
    crude <- gam(y ~ s(x1), family=binomial(link=logit), data=df)
    adj <- gam(y ~ s(x1) + s(x2), family=binomial(link=logit), data=df)

    # Plot results using 'visreg'
    library(visreg)
    p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), gg=TRUE) + theme_bw()
    p.adj <- visreg(adj, scale='response', "x1", gg=TRUE) + theme_bw()


    Using gridExtra I can produce a two columns plot, however I would have a single plot which overlays the two model plots.



    enter image description here










    share|improve this question
























      0












      0








      0







      I'm trying to draw in a single plot crude and adjusted GAM models using library visreg:



      # Create DF
      set.seed(123)
      x1 = rnorm(2000)
      z = 1 + 3*x1 + 3*exp(x1)
      pr = 1/(1+exp(-z))
      y = rbinom(2000,1,pr)
      df = data.frame(y=y,x1=x1, x2=exp(x1)*z)

      # Fitting GAMs
      library(mgcv)
      crude <- gam(y ~ s(x1), family=binomial(link=logit), data=df)
      adj <- gam(y ~ s(x1) + s(x2), family=binomial(link=logit), data=df)

      # Plot results using 'visreg'
      library(visreg)
      p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), gg=TRUE) + theme_bw()
      p.adj <- visreg(adj, scale='response', "x1", gg=TRUE) + theme_bw()


      Using gridExtra I can produce a two columns plot, however I would have a single plot which overlays the two model plots.



      enter image description here










      share|improve this question













      I'm trying to draw in a single plot crude and adjusted GAM models using library visreg:



      # Create DF
      set.seed(123)
      x1 = rnorm(2000)
      z = 1 + 3*x1 + 3*exp(x1)
      pr = 1/(1+exp(-z))
      y = rbinom(2000,1,pr)
      df = data.frame(y=y,x1=x1, x2=exp(x1)*z)

      # Fitting GAMs
      library(mgcv)
      crude <- gam(y ~ s(x1), family=binomial(link=logit), data=df)
      adj <- gam(y ~ s(x1) + s(x2), family=binomial(link=logit), data=df)

      # Plot results using 'visreg'
      library(visreg)
      p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), gg=TRUE) + theme_bw()
      p.adj <- visreg(adj, scale='response', "x1", gg=TRUE) + theme_bw()


      Using gridExtra I can produce a two columns plot, however I would have a single plot which overlays the two model plots.



      enter image description here







      r ggplot2 gridextra






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked Nov 11 at 15:44









      Borexino

      969




      969






















          1 Answer
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          You can use the plot=FALSE parameter to get the data without the plots:



          p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), plot=FALSE)
          p.adj <- visreg(adj, scale='response', "x1", plot = FALSE)


          And, then re-create it by hand:



          dplyr::bind_rows(
          dplyt::mutate(p.crude$fit, plt = "crude"),
          dplyr::mutate(p.adj$fit, plt = "adj")
          ) -> fits

          ggplot() +
          geom_ribbon(
          data = fits,
          aes(x1, ymin=visregLwr, ymax=visregUpr, group=plt), fill="gray90"
          ) +
          geom_line(data = fits, aes(x1, visregFit, group=plt, color=plt)) +
          theme_bw()


          enter image description here



          https://github.com/pbreheny/visreg/blob/master/R/ggFactorPlot.R has all the other computations and geoms/aesthetics you can use in the recreation.






          share|improve this answer




















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            1 Answer
            1






            active

            oldest

            votes








            1 Answer
            1






            active

            oldest

            votes









            active

            oldest

            votes






            active

            oldest

            votes









            1














            You can use the plot=FALSE parameter to get the data without the plots:



            p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), plot=FALSE)
            p.adj <- visreg(adj, scale='response', "x1", plot = FALSE)


            And, then re-create it by hand:



            dplyr::bind_rows(
            dplyt::mutate(p.crude$fit, plt = "crude"),
            dplyr::mutate(p.adj$fit, plt = "adj")
            ) -> fits

            ggplot() +
            geom_ribbon(
            data = fits,
            aes(x1, ymin=visregLwr, ymax=visregUpr, group=plt), fill="gray90"
            ) +
            geom_line(data = fits, aes(x1, visregFit, group=plt, color=plt)) +
            theme_bw()


            enter image description here



            https://github.com/pbreheny/visreg/blob/master/R/ggFactorPlot.R has all the other computations and geoms/aesthetics you can use in the recreation.






            share|improve this answer

























              1














              You can use the plot=FALSE parameter to get the data without the plots:



              p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), plot=FALSE)
              p.adj <- visreg(adj, scale='response', "x1", plot = FALSE)


              And, then re-create it by hand:



              dplyr::bind_rows(
              dplyt::mutate(p.crude$fit, plt = "crude"),
              dplyr::mutate(p.adj$fit, plt = "adj")
              ) -> fits

              ggplot() +
              geom_ribbon(
              data = fits,
              aes(x1, ymin=visregLwr, ymax=visregUpr, group=plt), fill="gray90"
              ) +
              geom_line(data = fits, aes(x1, visregFit, group=plt, color=plt)) +
              theme_bw()


              enter image description here



              https://github.com/pbreheny/visreg/blob/master/R/ggFactorPlot.R has all the other computations and geoms/aesthetics you can use in the recreation.






              share|improve this answer























                1












                1








                1






                You can use the plot=FALSE parameter to get the data without the plots:



                p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), plot=FALSE)
                p.adj <- visreg(adj, scale='response', "x1", plot = FALSE)


                And, then re-create it by hand:



                dplyr::bind_rows(
                dplyt::mutate(p.crude$fit, plt = "crude"),
                dplyr::mutate(p.adj$fit, plt = "adj")
                ) -> fits

                ggplot() +
                geom_ribbon(
                data = fits,
                aes(x1, ymin=visregLwr, ymax=visregUpr, group=plt), fill="gray90"
                ) +
                geom_line(data = fits, aes(x1, visregFit, group=plt, color=plt)) +
                theme_bw()


                enter image description here



                https://github.com/pbreheny/visreg/blob/master/R/ggFactorPlot.R has all the other computations and geoms/aesthetics you can use in the recreation.






                share|improve this answer












                You can use the plot=FALSE parameter to get the data without the plots:



                p.crude <- visreg(crude, scale='response', "x1", line.par = list(col = 'red'), plot=FALSE)
                p.adj <- visreg(adj, scale='response', "x1", plot = FALSE)


                And, then re-create it by hand:



                dplyr::bind_rows(
                dplyt::mutate(p.crude$fit, plt = "crude"),
                dplyr::mutate(p.adj$fit, plt = "adj")
                ) -> fits

                ggplot() +
                geom_ribbon(
                data = fits,
                aes(x1, ymin=visregLwr, ymax=visregUpr, group=plt), fill="gray90"
                ) +
                geom_line(data = fits, aes(x1, visregFit, group=plt, color=plt)) +
                theme_bw()


                enter image description here



                https://github.com/pbreheny/visreg/blob/master/R/ggFactorPlot.R has all the other computations and geoms/aesthetics you can use in the recreation.







                share|improve this answer












                share|improve this answer



                share|improve this answer










                answered Nov 11 at 16:02









                hrbrmstr

                60k685146




                60k685146



























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