05-02-2010
How to make a distance matrix
Hi,
I'm trying to generate a distance matrix between sample pairs for use in a tree-drawing program (example below). The example below demonstrates what I'd like to get out of the data - essentially, to calculate the proportion of positions where two samples differ.
Any help much appreciated! Also, any notes on how the functions work would be great!
Thanks!
Example input (note: comma indicates column separators, a:d are sample names):
a,1,2,4,4
b,2,1,4,4
c,1,2,3,4
d,1,0,4,0
Identify
positions which differ between pairwise comparisons of samples a:d (score 1 for differ, 0 for shared in example below)
some comparisons are duplicates, e.g. ab and ba, and self-comparisons such as aa or bb are obviously all "1", but these are neccessary to make the matrix
aa,1,1,1,1
ab,1,1,0,0
ac,0,0,1,0
ad,0,1,0,1
ba,1,1,0,0
bb,1,1,1,1
bc,1,1,1,0
etc... to dd
Calculate
proportion of differing positions between pairwise comparisons
aa,0
ab,0.5
ac,0.25
ad,0.5
ba,0.5
bb,0
bc,0.75
etc...to dd
prepare matrix (e.g. ab value plotted in [a,b]; ba value plotted in [b,a] etc...)
a,b,c,d
a,0,0.5,0.25,0.5
b,0.5,0,0.75 etc...
c
d
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LEARN ABOUT DEBIAN
gr_plot_fft_c
GR_PLOT_FFT_C(1) User Commands GR_PLOT_FFT_C(1)
NAME
gr_plot_fft_c - plot complex binary data using GNU Radio
SYNOPSIS
gr_plot_fft_c: [options] input_filename
DESCRIPTION
Takes a GNU Radio complex binary file and displays the I&Q data versus time as well as the frequency domain (FFT) plot. The y-axis values
are plotted assuming volts as the amplitude of the I&Q streams and converted into dBm in the frequency domain (the 1/N power adjustment out
of the FFT is performed internally). The script plots a certain block of data at a time, specified on the command line as -B or --block.
This value defaults to 1000. The start position in the file can be set by specifying -s or --start and defaults to 0 (the start of the
file). By default, the system assumes a sample rate of 1, so in time, each sample is plotted versus the sample number. To set a true time
and frequency axis, set the sample rate (-R or --sample-rate) to the sample rate used when capturing the samples.
OPTIONS
-h, --help
show this help message and exit
-B BLOCK, --block=BLOCK
Specify the block size [default=1000]
-s START, --start=START
Specify where to start in the file [default=0]
-R SAMPLE_RATE, --sample-rate=SAMPLE_RATE
Set the sampler rate of the data [default=1.0]
SEE ALSO
gr_plot_char(1) gr_plot_const(1) gr_plot_fft_c(1) gr_plot_fft_f(1) gr_plot_float(1) gr_plot_int(1) gr_plot_iq(1) gr_plot_psd_c(1)
gr_plot_psd_f(1) gr_plot_qt(1) gr_plot_short(1)
gr_plot_fft_c 3.5 December 2011 GR_PLOT_FFT_C(1)