Histogram with Logarithmic Scale and custom breaks

Question

I m trying to generate a histogram in R with a logarithmic scale for y  Currently I do   hist mydata V3  breaks c 0 1 2 3 4 5 25     This gives me a histogram  but the density between 0 to 1 is so great  about a million values difference  that you can barely make out any of the other bars   Then I ve tried doing   mydata hist  lt - hist mydata V3  breaks c 0 1 2 3 4 5 25   plot FALSE  plot rpd hist counts  log  xy   pch 20  col  blue     It gives me sorta what I want  but the bottom shows me the values 1-6 rather than 0  1  2  3  4  5  25   It s also showing the data as points rather than bars  barplot works but then I don t get any bottom axis

User · Accepted Answer

A histogram is a poor-man s density estimate   Note that in your call to hist   using default arguments  you get frequencies not probabilities -- add   prob TRUE to the call if you want probabilities     As for the log axis problem  don t use  x  if you do not want the x-axis transformed   plot mydata hist count  log  y   type  h   lwd 10  lend 2    gets you bars on a log-y scale -- the look-and-feel is still a little different but can probably be tweaked   Lastly  you can also do  hist log x         to get a histogram of the log of your data

User · Answer

Here s a pretty ggplot2 solution   library ggplot2  library scales     makes pretty labels on the x-axis  breaks c 0 1 2 3 4 5 25   ggplot mydata aes x   V3        geom histogram breaks   log10 breaks        scale x log10      breaks   breaks      labels   scales  trans format  log10   scales  math format 10  x         Note that to set the breaks in geom histogram  they had to be transformed to work with scale x log10

User · Answer

Another option would be to use the package ggplot2   ggplot mydata  aes x   V3     geom histogram     scale x log10

User · Answer

I ve put together a function that behaves identically to hist in the default case  but accepts the log argument  It uses several tricks from other posters  but adds a few of its own  hist x  and myhist x  look identical   The original problem would be solved with   myhist mydata V3  breaks c 0 1 2 3 4 5 25   log  xy     The function   myhist  lt - function x       breaks  Sturges                      main   paste  Histogram of   xname                      xlab   xname                     ylab    Frequency       xname   paste deparse substitute x   500   collapse   n     h   hist x  breaks breaks  plot FALSE    plot h breaks  c NA h counts   type  S   main main         xlab xlab  ylab ylab  axes FALSE         axis 1    axis 2    lines h breaks  c h counts NA   type  s     lines h breaks  c NA h counts   type  h     lines h breaks  c h counts NA   type  h     lines h breaks  rep 0 length h breaks    type  S     invisible h      Exercise for the reader  Unfortunately  not everything that works with hist works with myhist as it stands  That should be fixable with a bit more effort  though

User · Answer

It s not entirely clear from your question whether you want a logged x-axis or a logged y-axis   A logged y-axis is not a good idea when using bars because they are anchored at zero  which becomes negative infinity when logged   You can work around this problem by using a frequency polygon or density plot

User · Answer

Run the hist   function without making a graph  log-transform the counts  and then draw the figure   hist data   hist my data  plot F  hist data counts   log hist data counts  2  plot hist data    It should look just like the regular histogram  but the y-axis will be log2 Frequency

User · Answer

Dirk s answer is a great one  If you want an appearance like what hist produces  you can also try this   buckets  lt - c 0 1 2 3 4 5 25  mydata hist  lt - hist mydata V3  breaks buckets  plot FALSE  bp  lt - barplot mydata hist count  log  y   col  white   names arg buckets  text bp  mydata hist counts  labels mydata hist counts  pos 1    The last line is optional  it adds value labels just under the top of each bar  This can be useful for log scale graphs  but can also be omitted   I also pass main  xlab  and ylab parameters to provide a plot title  x-axis label  and y-axis label

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