From 1655d8ff7e5e9228a1c0c7ae65035e2787de33d7 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 10 Aug 2009 08:30:27 +0000 Subject: [PATCH] added --logscale_y switch to relevant plot_* biopieces git-svn-id: http://biopieces.googlecode.com/svn/trunk@628 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/plot_chrdist | 13 +++++++------ bp_bin/plot_histogram | 17 +++++++++-------- bp_bin/plot_lendist | 15 ++++++++------- bp_bin/plot_phastcons_profiles | 21 +++++++++++---------- code_perl/Maasha/Plot.pm | 4 ++++ 5 files changed, 39 insertions(+), 31 deletions(-) diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist index 9e3ba41..7d15721 100755 --- a/bp_bin/plot_chrdist +++ b/bp_bin/plot_chrdist @@ -42,12 +42,13 @@ $terminals = "dumb,x11,aqua,post,svg"; $options = Maasha::Biopieces::parse_options( [ - { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, - { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, - { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, + { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, + { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'logscale_y', short => 'L', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram index 4950305..7308c19 100755 --- a/bp_bin/plot_histogram +++ b/bp_bin/plot_histogram @@ -42,14 +42,15 @@ $terminals = "dumb,x11,aqua,post,svg"; $options = Maasha::Biopieces::parse_options( [ - { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, - { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, - { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, - { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'sort', short => 's', type => 'string', mandatory => 'no', default => 'alph', allowed => 'num,alph', disallowed => undef }, + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, + { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, + { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'sort', short => 's', type => 'string', mandatory => 'no', default => 'alph', allowed => 'num,alph', disallowed => undef }, + { long => 'logscale_y', short => 'L', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist index dfc0abb..58f9145 100755 --- a/bp_bin/plot_lendist +++ b/bp_bin/plot_lendist @@ -43,13 +43,14 @@ $terminals = "dumb,x11,aqua,post,svg"; $options = Maasha::Biopieces::parse_options( [ - { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, - { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, - { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, - { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, + { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, + { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'logscale_y', short => 'L', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles index 82db056..0fb79d1 100755 --- a/bp_bin/plot_phastcons_profiles +++ b/bp_bin/plot_phastcons_profiles @@ -46,16 +46,17 @@ $terminals = "dumb,x11,aqua,post,svg"; $options = Maasha::Biopieces::parse_options( [ - { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, - { long => 'mean', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'median', short => 'M', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, - { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, - { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, - { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'mean', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'median', short => 'M', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, + { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, + { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'logscale_y', short => 'L', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm index 94d542b..22968f3 100644 --- a/code_perl/Maasha/Plot.pm +++ b/code_perl/Maasha/Plot.pm @@ -90,6 +90,7 @@ sub lineplot_simple print $fh_in "set title \"$options->{ 'title' }\"\n" if $options->{ "title" }; print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" }; print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" }; + print $fh_in "set logscale y\n" if $options->{ "logscale_y" }; print $fh_in "set grid\n" if not $options->{ "terminal" } eq "dumb"; print $fh_in "set autoscale\n"; print $fh_in "unset key\n"; @@ -150,6 +151,7 @@ sub histogram_simple print $fh_in "set title \"$options->{ 'title' }\"\n" if $options->{ "title" }; print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" }; print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" }; + print $fh_in "set logscale y\n" if $options->{ "logscale_y" }; print $fh_in "set autoscale\n"; print $fh_in "unset key\n"; print $fh_in "set style fill solid\n"; @@ -227,6 +229,7 @@ sub histogram_lendist print $fh_in "set title \"$options->{ 'title' }\"\n" if $options->{ "title" }; print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" }; print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" }; + print $fh_in "set logscale y\n" if $options->{ "logscale_y" }; print $fh_in "set autoscale\n"; print $fh_in "unset key\n"; print $fh_in "set style fill solid\n"; @@ -284,6 +287,7 @@ sub histogram_chrdist print $fh_in "set title \"$options->{ 'title' }\"\n" if $options->{ "title" }; print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" }; print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" }; + print $fh_in "set logscale y\n" if $options->{ "logscale_y" }; print $fh_in "set autoscale\n"; print $fh_in "unset key\n"; print $fh_in "set style fill solid\n"; -- 2.39.5