Mercurial > repos > bgruening > upload_testing
changeset 83:4a25bb3a8c69 draft
Uploaded
| author | bernhardlutz |
|---|---|
| date | Mon, 20 Jan 2014 16:19:34 -0500 |
| parents | 057169fb41c7 |
| children | 5e3fccdcd9a0 |
| files | cor.xml histogram.xml scatterplot.xml short_reads_figure_score.xml static/images/histogram2.png static/images/kendall.png static/images/pearson.png static/images/scatterplot.png static/images/spearman.png tool_dependencies.xml |
| diffstat | 10 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/cor.xml Mon Jan 20 15:08:40 2014 -0500 +++ b/cor.xml Mon Jan 20 16:19:34 2014 -0500 @@ -48,19 +48,19 @@ - **Pearson's Correlation** reflects the degree of linear relationship between two variables. It ranges from +1 to -1. A correlation of +1 means that there is a perfect positive linear relationship between variables. The formula for Pearson's correlation is: - .. image:: ${static_path}/images/pearson.png + .. image:: $PATH_TO_IMAGES/pearson.png where n is the number of items - **Kendall's rank correlation** is used to measure the degree of correspondence between two rankings and assessing the significance of this correspondence. The formula for Kendall's rank correlation is: - .. image:: ${static_path}/images/kendall.png + .. image:: $PATH_TO_IMAGES/kendall.png where n is the number of items, and P is the sum. - **Spearman's rank correlation** assesses how well an arbitrary monotonic function could describe the relationship between two variables, without making any assumptions about the frequency distribution of the variables. The formula for Spearman's rank correlation is - .. image:: ${static_path}/images/spearman.png + .. image:: $PATH_TO_IMAGES/spearman.png where D is the difference between the ranks of corresponding values of X and Y, and N is the number of pairs of values.
--- a/histogram.xml Mon Jan 20 15:08:40 2014 -0500 +++ b/histogram.xml Mon Jan 20 16:19:34 2014 -0500 @@ -71,7 +71,7 @@ - Create a histogram on column 2 of the above dataset. -.. image:: ${static_path}/images/histogram2.png +.. image:: $PATH_TO_IMAGES/histogram2.png </help> </tool>
--- a/scatterplot.xml Mon Jan 20 15:08:40 2014 -0500 +++ b/scatterplot.xml Mon Jan 20 16:19:34 2014 -0500 @@ -64,7 +64,7 @@ - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset. -.. image:: ${static_path}/images/scatterplot.png +.. image:: $PATH_TO_IMAGES/images/scatterplot.png </help> </tool>
--- a/short_reads_figure_score.xml Mon Jan 20 15:08:40 2014 -0500 +++ b/short_reads_figure_score.xml Mon Jan 20 16:19:34 2014 -0500 @@ -56,7 +56,7 @@ Quality scores are summarized as boxplot (Roche 454 FLX data): -.. image:: ${static_path}/images/short_reads_boxplot.png +.. image:: $PATH_TO_IMAGES/short_reads_boxplot.png where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines:
--- a/tool_dependencies.xml Mon Jan 20 15:08:40 2014 -0500 +++ b/tool_dependencies.xml Mon Jan 20 16:19:34 2014 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7c6ec22e9ef0" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="rpy2_2_3_6" version="2.3.6"> <repository changeset_revision="ef3a897cf4f2" name="package_rpy2_2_3_6" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />