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quick_plot

quick_plot is a python script that uses matplotlib to create simple visualizations of data from the command line.

Author

Dent Earl

Dependencies

Installation

  1. Download the package.
  2. cd into the directory.
  3. Type make.

Input file format

The input file may contain comment lines (lines that start with #). Files may contain one or more columns (white space delimited) of numbers

Usage

usage: quick_plot file1 file2 file3... [options]

quick_plot is a tool to produce quick plots. col1 of input file is x value col2 is y
value. If the --mode is column/bar/hist then only col1 is used.

positional arguments:
  files                 files to plot

optional arguments:
  -h, --help            show this help message and exit
  --out OUT             path/filename where figure will be created. No extension needed.
                        default=my_plot
  --mode MODE           plotting mode. may be in (line, scatter, column, bar, hist, tick, barcode,
                        point, contour, density, matrix) default=line
  --columns COLUMNS     two numbers, comma separated, can be reverse order, indicates x,y for
                        plotting. 1-based.
  --downsample DOWNSAMPLE
                        Randomly sample only n values from each input. Can help cutdown on runtime
                        and output size for pdfs.
  --colors COLORS       color palatte mode. may be in (bostock, brewer, mono, hcl_ggplot2)
                        default=brewer
  --color_index_offset COLOR_INDEX_OFFSET
                        index offset value to shift the starting point of the selected color map.
                        default=0
  --alpha ALPHA         alpha value for markers in --mode scatter
  --dot_size MARKERSIZE, --markersize MARKERSIZE
                        value for markers in --mode scatter
  --marker MARKER       Marker to use.
  --linewidth LINEWIDTH
                        Line width for the plot. default=2.0
  --logy                Put the y-axis into log. default=False
  --logx                Put the x-axis into log. default=False
  --title TITLE         Plot title.
  --xlabel XLABEL       X-axis label.
  --ylabel YLABEL       Y-axis label.
  --xmin USER_XMIN      xmin value.
  --xmax USER_XMAX      xmax value.
  --ymin USER_YMIN      ymin value.
  --ymax USER_YMAX      ymax value.
  --height HEIGHT       height of image, in inches. default=4.0
  --width WIDTH         width of image, in inches. default=9.0
  --dpi DPI             dots per inch of raster outputs, i.e. if --outFormat is all or png.
                        default=300
  --out_format OUT_FORMAT
                        output format [pdf|png|eps|all]. default=pdf
  --no_legend           Turns off the filename / color legend. Helpful for large numbers of files.
  --regression          turn on a simple linear regression line
  --jitter              turn on jitter for certain plotting modes
  --random_seed RANDOM_SEED
                        Random seed for use with --jitter and --downsample flags.
  --aspect_equal        Turn on equal aspect ratio for the plot

contour mode:
  --contour_bin CONTOUR_BIN
                        Bin size of the contour plot. Smaller integers lead to smoother curves.
  --contour_logspace    Switch the contour lines from linear spacing to log spacing
  --contour_num_levels CONTOUR_NUM_LEVELS
                        The number of levels in the contour plot, default=6

density mode:
  --density_covariance DENSITY_COVARIANCE
                        Gaussian kernel density estimate covariance, raising the value leads to
                        smoother curves. This roughly corresponds to bandwidth in R. Default is to
                        discover the value automatically.
  --density_num_bins DENSITY_NUM_BINS
                        Number of "bins" for the density curve. default=200

matrix mode:
  --matrix_matshow      Switches the drawing call from pcolor() to matshow(). matshow() uses rasters,
                        pcolor() uses vectors. For very large matrices matshow() may be desirable.
  --matrix_cmap MATRIX_CMAP
                        The colormap to be used. default=binary. Possible values: Spectral, summer,
                        coolwarm, Set1, Set2, Set3, Dark2, hot, RdPu, YlGnBu, RdYlBu, gist_stern,
                        cool, gray, GnBu, gist_ncar, gist_rainbow, bone, RdYlGn, spring, terrain,
                        PuBu, spectral, gist_yarg, BuGn, bwr, cubehelix, YlOrRd, Greens, PRGn,
                        gist_heat, Paired, hsv, Pastel2, Pastel1, BuPu, copper, OrRd, brg, gnuplot2,
                        jet, gist_earth, Oranges, PiYG, YlGn, Accent, gist_gray, flag, BrBG, Reds,
                        RdGy, PuRd, Blues, Greys, autumn, pink, binary, winter, gnuplot, RdBu, prism,
                        YlOrBr, rainbow, seismic, Purples, ocean, PuOr, PuBuGn, afmhot
  --matrix_no_colorbar  turn off the colorbar.
  --matrix_discritize_colormap MATRIX_DISCRITIZE_COLORMAP
                        number of bins to discritize colormap

Examples

Plotting 2D scatter data, one file, no legend.

bin/quick_plot example/data_2d_1.txt --mode scatter --markersize 7.0 --out_format png --out img/example_01.png --title '2D scatter data from example/data_2d_1.txt' --xlabel 'The x-axis' --ylabel 'The y-axis' --no_legend

Example image

Plotting 2D scatter data, two files.

bin/quick_plot example/data_2d_1.txt example/data_2d_2.txt --mode scatter --markersize 7.0 --out_format png --out img/example_02.png

Example image

Plotting 2D line data, two files.

bin/quick_plot example/data_2d_3.txt example/data_2d_4.txt --mode line --out_format png --out img/example_03.png

Example image

Plotting 2D line data, three files.

bin/quick_plot example/data_2d_5.txt example/data_2d_6.txt example/data_2d_7.txt --mode line --out_format png --out img/example_04.png

Example image

Plotting 1D data as bars, two files.

bin/quick_plot example/data_1d_1.txt example/data_1d_2.txt --mode bar --out_format png --out img/example_05.png

Example image

Plotting 1D data as tick marks, two files.

bin/quick_plot example/data_1d_1.txt example/data_1d_2.txt --mode tick --out_format png --out img/example_06.png

Example image

Plotting 1D data as point marks, two files.

bin/quick_plot example/data_1d_1.txt example/data_1d_2.txt --mode point --out_format png --out img/example_07.png

Example image

Plotting 1D data as point clouds (using jitter), two files.

(Remove the --random_seed for production use).

bin/quick_plot example/data_1d_1.txt example/data_1d_2.txt --mode point --jitter --out_format png --out img/example_08.png --random_seed=127

Example image

Plotting 1D data as histogram, three files.

bin/quick_plot example/data_1d_3.txt example/data_1d_4.txt example/data_1d_5.txt --mode hist --out_format png --out img/example_09.png

Example image

Plotting 2D data as scatter plot, one file.

bin/quick_plot example/data_2d_8.txt --mode scatter --markersize 5.0 --out_format png --out img/example_10.png

Example image

Plotting 2D data as scatter plot with alpha transparency, one file.

bin/quick_plot example/data_2d_8.txt --mode scatter --markersize 5.0 --alpha 0.1 --out_format png --out img/example_11.png

Example image

Plotting 2D data as scatter plot with alpha transparency, fixing the aspect ratio, one file.

bin/quick_plot example/data_2d_8.txt --mode scatter --markersize 5.0 --alpha 0.1 --out_format png --out img/example_11_a.png --aspect_equal

Example image

Plotting 2D data as scatter plot using downsampling to 1000 points, fixing the aspect ratio, one file.

(Remove the --random_seed for production use).

bin/quick_plot example/data_2d_8.txt --mode scatter --markersize 5.0 --out_format png --out img/example_11_b.png --aspect_equal --random_seed=127 --downsample 1000 --title 'Downsampled to 1000 points'

Example image

Plotting 2D data as scatter plot using downsampling to 100 points, fixing the aspect ratio, one file.

(Remove the --random_seed for production use).

bin/quick_plot example/data_2d_8.txt --mode scatter --markersize 5.0 --alpha 0.1 --out_format png --out img/example_11_c.png --aspect_equal --random_seed=127 --downsample 100 --title 'Downsampled to 100 points'

Example image

Plotting 1D data as density curve, one file.

bin/quick_plot example/data_1d_7.txt --mode density --out_format png --out img/example_12.png --title 'data_2d_8.txt x marginal'

Example image

Plotting 1D data as density curve, one file, selecting column to plot.

bin/quick_plot example/data_2d_8.txt --mode density --out_format png --out img/example_12_a.png --title 'data_2d_8.txt x marginal' --columns 1

Example image

Plotting 1D data as density curve, one file.

bin/quick_plot example/data_1d_8.txt --mode density --out_format png --out img/example_13.png --title 'data_2d_8.txt y marginal'

Example image

Plotting 1D data as density curve, one file, selecting column to plot.

bin/quick_plot example/data_1d_8.txt --mode density --out_format png --out img/example_13_a.png --title 'data_2d_8.txt y marginal' --columns 2

Example image

Plotting 2D data as contour plot, one file.

bin/quick_plot example/data_2d_8.txt --mode contour --out_format png --out img/example_14.png --title 'A hard example for a contour plot'

Example image

Plotting 2D data as contour plot, one file.

bin/quick_plot example/data_2d_9.txt --mode contour --out_format png --out img/example_15.png --title 'An easier example for a contour plot'

Example image

Anscombe's quartet, plotting from a single file with many columns, mixing and matching columns

bin/quick_plot example/anscombe.txt --mode scatter --out_format png --out img/example_16.png --title 'Anscombe_i' --regression  --markersize 5.0 --ymin 3 --ymax 13 --xmin 3 --xmax 20 --no_legend

Example image

bin/quick_plot example/anscombe.txt --mode scatter --out_format png --out img/example_17.png --title 'Anscombe_ii' --regression  --markersize 5.0 --ymin 3 --ymax 13 --xmin 3 --xmax 20 --no_legend --columns 3,4

Example image

bin/quick_plot example/anscombe.txt --mode scatter --out_format png --out img/example_18.png --title 'Anscombe_iii' --regression  --markersize 5.0 --ymin 3 --ymax 13 --xmin 3 --xmax 20 --no_legend --columns 5,6

Example image

bin/quick_plot example/anscombe.txt --mode scatter --out_format png --out img/example_19.png --title 'Anscombe_iiv' --regression  --markersize 5.0 --ymin 3 --ymax 13 --xmin 3 --xmax 20 --no_legend --columns 7,8

Example image

Matrix plot (heatmap) using a continuous colormap

bin/quick_plot example/distance_matrix.txt --mode matrix --out_format png --out img/example_20.png --title 'Heatmap' --matrix_cmap Reds --width 6

Example image

Matrix plot (heatmap) using a continuous colormap, censoring colormap

bin/quick_plot example/distance_matrix.txt --mode matrix --out_format png --out img/example_20_a.png --title 'Heatmap' --matrix_cmap Reds --width 6 --matrix_colormap_max 0.20

Example image

Heatmap using a discritized colormap

bin/quick_plot example/distance_matrix_1.txt --mode matrix --out_format png --out img/example_21.png --title 'Heatmap 2' --width 6 --matrix_discritize_colormap 6

Example image

Heatmap using a discritized colormap without a colorbar

bin/quick_plot example/distance_matrix_2.txt --mode matrix --out_format png --out img/example_22.png --title 'Heatmap 3' --matrix_cmap Oranges --width 6 --matrix_discritize_colormap 10 --matrix_no_colorbar

Example image