Mean & error bars

Graphs with mean and error bars: SD, SEM or CI95.

Changing error bars

Version 3.1.0 onwards, error bars can be changed from the default SD (sample standard deviation) to SEM (standard error of the mean) or CI95 (95% confidence intervals based on t distributions). These are implemented through mean_sdl (with multi = 1), mean_se and mean_cl_normal from Hmisc.

Data format

All plot_ functions require a long-format data table as the first argument, followed by the name of the column (a categorical variable) to be plotted on the X-axis (xcol) and the quantitative variable to be plotted on the Y-axis (ycol). If provided in this order the data =, xcol = and ycol = need not be explicitly called (see examples below).

See the data help page and ensure data table is in the long-format.

Saving graphs

See Saving graphs for tips on how to save plots for making figures.

Different types of error bars

ErrorType argument

Error bars can be changed in plot_point_sd, plot_scatterbar_sd, plot_3d_scatterbar, plot_4d_scatterbar, plot_dotbar_sd. In all cases, ErrorType is the argument after facet.

The acceptable inputs are “SD”, “SEM” or “CI95”. Some examples are shown below.

#default SD error bars
plot_scatterbar_sd(data = data_1w_death, #data table
                   xcol = Genotype,      #X variable
                   ycol = Death,         #Y variable
                   fontsize = 25)+
  labs(title = "Scatter and bar with error bars", #title 
       subtitle = "(default SD error bars)")+
  guides(fill = "none")

#SEM error bars
plot_scatterbar_sd(data = data_1w_death, #data table
                   xcol = Genotype,      #X variable
                   ycol = Death,         #Y variable
                   fontsize = 25,
                   ErrorType = "SEM")+   #SEM error bars
  labs(title = "Scatter and bar with error bars", #title 
       subtitle = "(SEM error bars)")+
  guides(fill = "none")

#CI95 error bars
plot_scatterbar_sd(data = data_1w_death, #data table
                   xcol = Genotype,      #X variable
                   ycol = Death,         #Y variable
                   fontsize = 25,
                   ErrorType = "CI95")+  #CI95 error bars
  labs(title = "Scatter and bar with error bars", #title 
       subtitle = "(CI95 error bars)")+
  guides(fill = "none")

plot_point_sd

Since v3.1.0, this function also allows the user to show all data points in addition to a large symbol for the mean. Error bars can now be changed from default “SD” to “SEM or”CI95”.

Example below with palmerpenguins dataset.

plot_point_sd(penguins,
            species,
            body_mass_g, 
            sex,                 #facet
            all_alpha = 0.5,     #opacity for all data
            all_jitter = 0.2,    #jitter for all data
            ColPal = "bright", 
            TextXAngle = 45,
            fontsize = 25)+
  labs(title = "Mean & SD",
       subtitle = "(showing all data points)")+
  guides(fill = "none")

plot_point_sd(penguins,
            species,
            body_mass_g, 
            sex,                 #facet
            all_alpha = 0.5,     #opacity for all data
            all_jitter = 0.2,    #jitter for all data
            ErrorType = "CI95",  #CI95 error bars
            ColPal = "bright", 
            TextXAngle = 45,
            fontsize = 25)+
  labs(title = "Mean & CI95",
       subtitle = "(showing all data points)")+
  guides(fill = "none")