Scatter plot with error bars

Question

How can I generate the following plot in R  Points  shown in the plot are the averages  and their ranges correspond to minimal and maximal values  I have data in two files  below is an example     x   y 1   0 8773 1   0 8722 1   0 8816 1   0 8834 1   0 8759 1   0 8890 1   0 8727 2   0 9047 2   0 9062 2   0 8998 2   0 9044 2   0 8960

User · Answer

To summarize Laryx Decidua s answer   define and use a function like the following  plot with errorbars  lt - function x  y  err  ylim NULL           if  is null ylim       ylim  lt - c min y-err   max y err     plot x  y  ylim ylim  pch 19         arrows x  y-err  x  y err  length 0 05  angle 90  code 3      where one can override the automatic ylim  and also pass extra parameters such as main  xlab  ylab

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Using ggplot and a little dplyr for data manipulation   set seed 42  df  lt - data frame x   rep 1 10 each 5   y   rnorm 50    library ggplot2  library dplyr   df summary  lt - df   gt   group by x    gt       summarize ymin   min y                 ymax   max y                 ymean   mean y    ggplot df summary  aes x   x  y   ymean         geom point size   2        geom errorbar aes ymin   ymin  ymax   ymax     If there s an additional grouping column  OP s example plot has two errorbars per x value  saying the data is sourced from two files   then you should get all the data in one data frame at the start  add the grouping variable to the dplyr  group by call  e g   group by x  file  if file is the name of the column  and add it as a  group  aesthetic in the ggplot  e g   aes x   x  y   ymean  group   file

User · Answer

Another  easier - at least for me  way to do this is below   install packages  ggplot2movies    data movies  package  ggplot2movies     Plot average Length vs Rating  rating by len   tapply movies length                         movies rating                         mean   plot names rating by len   rating by len  ylim c 0  200        xlab    Rating   ylab    Length   main  Average Rating by Movie Length   pch 21    Add error bars to the plot  mean - sd  mean   sd  sds   tapply movies length  movies rating  sd  upper   rating by len   sds lower   rating by len - sds segments x0 as numeric names rating by len              y0 lower            y1 upper    Hope that helps

User · Answer

First of all  it is very unfortunate and surprising that R cannot draw error bars  out of the box    Here is my favourite workaround  the advantage is that you do not need any extra packages  The trick is to draw arrows     but with little horizontal bars instead of arrowheads        This not-so-straightforward idea comes from the R Wiki Tips and is reproduced here as a worked-out example   Let s assume you have a vector of  average values  avg and another vector of  standard deviations  sdev  they are of the same length n  Let s make the abscissa just the number of these  measurements   so x  lt - 1 n  Using these  here come the plotting commands   plot x  avg      ylim range c avg-sdev  avg sdev        pch 19  xlab  Measurements   ylab  Mean   - SD       main  Scatter plot with std dev error bars      hack  we draw arrows but with very special  arrowheads  arrows x  avg-sdev  x  avg sdev  length 0 05  angle 90  code 3    The result looks like this     In the arrows      function length 0 05 is the size of the  arrowhead  in inches  angle 90 specifies that the  arrowhead  is perpendicular to the shaft of the arrow  and the particularly intuitive code 3 parameter specifies that we want to draw an arrowhead on both ends of the arrow   For horizontal error bars the following changes are necessary  assuming that the sdev vector now contains the errors in the x values and the y values are the ordinates   plot x  y      xlim range c x-sdev  x sdev        pch 19        horizontal error bars arrows x-sdev  y  x sdev  y  length 0 05  angle 90  code 3

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some example data set seed 42  df  lt - data frame x   rep 1 10 each 5   y   rnorm 50     calculate mean  min and max for each x-value library plyr  df2  lt - ddply df   x  function df  c mean mean df y  min min df y  max max df y      plot error bars library Hmisc  with df2 errbar x mean max min   grid nx NA ny NULL

User · Answer

I put together start to finish code of a hypothetical experiment with ten measurement replicated three times  Just for fun with the help of other stackoverflowers  Thank you    Obviously loops are an option as applycan be used but I like to see what happens    Create fake data x  lt -rep 1 10  each  3  y  lt - rnorm 30  mean 4 sd 1    Loop to get standard deviation from data sd y   NULL for i in 1 10     sd y i   lt - sd y  1  i-1  3   3  i-1  3      sd y lt -rep sd y each   3    Loop to get mean from data mean y   NULL for i in 1 10     mean y i   lt - mean y  1  i-1  3   3  i-1  3      mean y lt -rep mean y each   3    Put together the data to view it so far data  lt - cbind x  y  mean y  sd y    Make an empty matrix to fill with shrunk data data 1   matrix data   NA  nrow 10  ncol   4  colnames data 1   lt - c  X   Y   MEAN   SD     Loop to put data into shrunk format for i in 1 10     data 1 i    lt - data  1  i-1  3        Create atomic vectors for arrows x  lt - data 1  1  mean exp  lt - data 1  3  sd exp  lt - data 1  4    Plot the data plot x  mean exp  ylim   range c mean exp-sd exp mean exp sd exp    abline h   4  arrows x  mean exp-sd exp  x  mean exp sd exp  length 0 05  angle 90  code 3

[r] Scatter plot with error bars

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