Module: FeldtRuby::Statistics::Plotting

Included in:
RCommunicator
Defined in:
lib/feldtruby/statistics.rb

Overview

Plotting data sets in R with ggplot2 and save them to files.

Constant Summary collapse

GfxFormatToGfxParams = 
{
  "pdf" => {:width => 7, :height => 5, :paper => 'special'},
  "png" => {:units => "cm", :width => 12, :height => 8},
  "tiff" => {:units => "cm", :width => 12, :height => 8},
}

Instance Method Summary collapse

Instance Method Details

#density_tile2d(csvFilePath, xlabel, ylabel, title = "densitytile2d") ⇒ Object 



359
360
361
362
363
364
365
366
367
368
 
# File 'lib/feldtruby/statistics.rb', line 359

def density_tile2d(csvFilePath, xlabel, ylabel, title = "densitytile2d")

  script = <<-EOS
    f <- ggplot(data, aes(x=#{xlabel}, y=#{ylabel}))
    f <- f + stat_density2d(geom="tile", aes(fill=..density..), contour=FALSE) + scale_fill_gradient(high="red", low="white")
  EOS

  plot_2dims(csvFilePath, script, xlabel.to_s, ylabel.to_s, title)

end

#filled_contour(csvFilePath, xlabel, ylabel, title = "filled.contour") ⇒ Object 



275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
 
# File 'lib/feldtruby/statistics.rb', line 275

def filled_contour(csvFilePath, xlabel, ylabel, title = "filled.contour")
  include_library "MASS"

  script = <<-EOS
    data <- read.csv(#{csvFilePath.inspect})
    k <- with(data, MASS::kde2d(#{xlabel}, #{ylabel}))
    f <- filled.contour(k, color=topo.colors, 
           plot.title=title(main = _title_),
           xlab=_xlabel_, ylab=_ylabel_)
    f
  EOS

  subst_eval script, {:title => title,
    :xlabel => xlabel.to_s, :ylabel => ylabel.to_s}

end

#gfx_device(format, width = nil, height = nil) ⇒ Object 



236
237
238
239
240
241
242
243
244
245
246
247
248
 
# File 'lib/feldtruby/statistics.rb', line 236

def gfx_device(format, width = nil, height = nil)

  format = format.to_s            # If given as a symbol instead of a string

  unless GfxFormatToGfxParams.has_key?(format)
    raise ArgumentError.new("Don't now about gfx format #{format}")
  end

  params = GfxFormatToGfxParams[format]

  "#{format}(#{hash_to_R_params(params)})"

end

#ggplot2_setup_and_theme ⇒ Object 



398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
 
# File 'lib/feldtruby/statistics.rb', line 398

def ggplot2_setup_and_theme

  include_library("ggplot2")
  include_library("reshape2")

  script = <<-EOS
    f <- f + ggtitle(_title_) + xlab(_xlabel_) + ylab(_ylabel_)
    f <- f + theme_bw()
    f <- f + theme(
            plot.title = element_text(face="bold", size=12), 
            axis.title.x = element_text(face="bold", size=10),
            axis.title.y = element_text(face="bold", size=10)
          )
  EOS

end

#hash_to_R_params(hash) ⇒ Object

Map a ruby hash of objects to parameters in R code/script.



251
252
253
254
255
256
257
258
259
 
# File 'lib/feldtruby/statistics.rb', line 251

def hash_to_R_params(hash)

  hash.keys.sort.map do |key|

    "#{key.to_s} = #{ruby_object_to_R_string(hash[key])}"

  end.join(", ")

end

#hexbin_heatmap(csvFilePath, xlabel, ylabel, title = "heatmap", bins = 50) ⇒ Object 



303
304
305
306
307
308
309
310
311
 
# File 'lib/feldtruby/statistics.rb', line 303

def hexbin_heatmap(csvFilePath, xlabel, ylabel, title = "heatmap", bins = 50)
  include_library "grid"
  include_library "lattice"
  include_library "hexbin"

  plot_2dims(csvFilePath,
    "f <- ggplot(data, aes(#{xlabel}, #{ylabel})) + geom_hex( bins = #{bins} )",
    xlabel, ylabel, title)
end

#load_csv_files_as_data(dataMap, columnName = nil) ⇒ Object

Data can be specified in two ways, either directly in Ruby arrays, or as strings with the path to a csv file to be loaded. In the latter case a column name must be given.



328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
 
# File 'lib/feldtruby/statistics.rb', line 328

def load_csv_files_as_data(dataMap, columnName = nil)

  keys = dataMap.keys.sort

  read_csvs = ""
  data_frame = "data.frame(1:length(d_#{keys.first})"

  keys.each_with_index do |key, i|

    value = dataMap[key]

    set_name = "d_#{key}"
    
    read_csvs += "#{set_name} <- "

    if Array === value
      read_csvs += (ruby_object_to_R_string(value) + ";\n")
      data_frame += ", #{key} = #{set_name}"
    else
      read_csvs += "read.csv(#{value.inspect});\n"
      data_frame += ", #{key} = #{set_name}$#{columnName}"
    end

  end

  data_frame += ")"

  script = "#{read_csvs}data <- #{data_frame};"

end

#overlaid_densities(dataMap, title = "Densities of distributions", datasetsName = "distribution", xlabel = "values", ylabel = "density") ⇒ Object

Overlaid density graph of the observations (sampled distributions) in data1 and data2. The dataMap maps the name of each data series to an array with its observations.



418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
 
# File 'lib/feldtruby/statistics.rb', line 418

def overlaid_densities(dataMap, title = "Densities of distributions", datasetsName = "distribution", xlabel = "values", ylabel = "density")

  cardinalities = dataMap.values.map {|vs| vs.length}.uniq

  unless cardinalities.length == 1

    raise ArgumentError.new("Must have same cardinality")

  end

  script = <<-EOS
    df <- data.frame(index = (1:#{cardinalities.first}), #{hash_to_R_params(dataMap)})
    df.m <- melt(df, id = "index")
    names(df.m)[2] <- _datasetsName_
    f <- ggplot(df.m, aes(value, fill=#{datasetsName}))
    f <- f + geom_density(alpha = 0.2, size = 0.5) + scale_color_brewer()
    #{ggplot2_setup_and_theme()}
    f
  EOS

  subst_eval script, {:title => title, :datasetsName => datasetsName,
    :xlabel => xlabel, :ylabel => ylabel}

end

#overlaid_densities_from_csv_files(columnName, csvFiles, title = "Densities of distributions", datasetsName = "distribution", xlabel = "values", ylabel = "density") ⇒ Object

Plot the densities of the data found in the column named columnName in the csv files in csvFiles.



445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
 
# File 'lib/feldtruby/statistics.rb', line 445

def overlaid_densities_from_csv_files(columnName, csvFiles, title = "Densities of distributions", datasetsName = "distribution", xlabel = "values", ylabel = "density")

  load_csvs = load_csv_files_as_data csvFiles

  script = <<-EOS
    #{load_csvs}
    #df <- data.frame(index = (1:#{cardinalities.first}), #{hash_to_R_params(dataMap)})
    df.m <- melt(df, id = "index")
    names(df.m)[2] <- _datasetsName_
    f <- ggplot(df.m, aes(value, fill=#{datasetsName}))
    f <- f + geom_density(alpha = 0.2, size = 0.5) + scale_color_brewer()
    #{ggplot2_setup_and_theme()}
    f
  EOS

  puts script
  subst_eval script, {:title => title, :datasetsName => datasetsName,
    :xlabel => xlabel, :ylabel => ylabel}

end

#plot_2dims(csvFilePath, plotCommand, xlabel, ylabel, title = "scatterplot") ⇒ Object 



261
262
263
264
265
266
267
268
269
270
271
272
273
 
# File 'lib/feldtruby/statistics.rb', line 261

def plot_2dims(csvFilePath, plotCommand, xlabel, ylabel, title = "scatterplot")

  script = <<-EOS
    data <- read.csv(#{csvFilePath.inspect})
    #{plotCommand}
    #{ggplot2_setup_and_theme()}
    f
  EOS

  subst_eval script, {:title => title,
    :xlabel => xlabel, :ylabel => ylabel}

end

#save_graph(filename, width = nil, height = nil) ⇒ Object

Wrap a sve_graph call around a block that draws a diagram and this will save the diagram to a file. The filetype is given by the file ending of the file name.



379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
 
# File 'lib/feldtruby/statistics.rb', line 379

def save_graph(filename, width = nil, height = nil)

  file_ending = filename.split(".").last

  raise "Don't now about graphics format #{file_ending}" unless GfxFormatToGfxParams.has_key?(file_ending)

  params = GfxFormatToGfxParams[file_ending].clone

  params[:width] = width if width
  params[:height] = height if height

  RC.eval("#{file_ending}(#{filename.inspect}, #{hash_to_R_params(params)})")

  yield() # Just be sure not to nest these save_graph calls within each other...

  RC.eval("dev.off()")

end

#scatter_plot(csvFilePath, xlabel, ylabel, title = "scatterplot") ⇒ Object 



313
314
315
316
317
318
319
320
321
322
323
 
# File 'lib/feldtruby/statistics.rb', line 313

def scatter_plot(csvFilePath, xlabel, ylabel, title = "scatterplot")

  script = <<-EOS
    smoothing_method <- if(nrow(data) > 1000) {'gam'} else {'loess'}
    f <- ggplot(data, aes(#{xlabel}, #{ylabel})) + geom_point(shape = 1)
    f <- f + stat_smooth(method = smoothing_method)
  EOS

  plot_2dims(csvFilePath, script, xlabel.to_s, ylabel.to_s, title)

end

#smooth_scatter_plot(csvFilePath, xlabel, ylabel, title = "smoothscatter") ⇒ Object 



292
293
294
295
296
297
298
299
300
301
 
# File 'lib/feldtruby/statistics.rb', line 292

def smooth_scatter_plot(csvFilePath, xlabel, ylabel, title = "smoothscatter")
  include_library "graphics"

  script = <<-EOS
    f <- ggplot(data, aes(#{xlabel}, #{ylabel})) +
           geom_point() + geom_smooth( method="loess", se = FALSE )
  EOS

  plot_2dims(csvFilePath, script, xlabel.to_s, ylabel.to_s, title)
end