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Merge pull request #140 from lukenoaa/master
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add new notebook tourmaline_taxonomy_notebook.ipynb #139 #113, delete…
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@lukenoaa
lukenoaa authored Jul 25, 2024
2 parents 3dcffca + 58a508f commit e928a3a
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9 changes: 0 additions & 9 deletions Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ rule dada2_pe_diversity_unfiltered:
"02-output-dada2-pe-unfiltered/03-alpha-diversity/faith_pd_group_significance.qzv",
"02-output-dada2-pe-unfiltered/03-alpha-diversity/observed_features_group_significance.qzv",
"02-output-dada2-pe-unfiltered/03-alpha-diversity/shannon_group_significance.qzv",
"02-output-dada2-pe-unfiltered/03-alpha-diversity/evenness_group_significance.qzv",
"02-output-dada2-pe-unfiltered/04-beta-diversity/bray_curtis_emperor.qzv",
"02-output-dada2-pe-unfiltered/04-beta-diversity/bray_curtis_group_significance.qzv",
"02-output-dada2-pe-unfiltered/04-beta-diversity/jaccard_emperor.qzv",
Expand Down Expand Up @@ -90,7 +89,6 @@ rule dada2_pe_diversity_filtered:
"02-output-dada2-pe-filtered/03-alpha-diversity/faith_pd_group_significance.qzv",
"02-output-dada2-pe-filtered/03-alpha-diversity/observed_features_group_significance.qzv",
"02-output-dada2-pe-filtered/03-alpha-diversity/shannon_group_significance.qzv",
"02-output-dada2-pe-filtered/03-alpha-diversity/evenness_group_significance.qzv",
"02-output-dada2-pe-filtered/04-beta-diversity/bray_curtis_emperor.qzv",
"02-output-dada2-pe-filtered/04-beta-diversity/bray_curtis_group_significance.qzv",
"02-output-dada2-pe-filtered/04-beta-diversity/jaccard_emperor.qzv",
Expand Down Expand Up @@ -141,7 +139,6 @@ rule dada2_se_diversity_unfiltered:
"02-output-dada2-se-unfiltered/03-alpha-diversity/faith_pd_group_significance.qzv",
"02-output-dada2-se-unfiltered/03-alpha-diversity/observed_features_group_significance.qzv",
"02-output-dada2-se-unfiltered/03-alpha-diversity/shannon_group_significance.qzv",
"02-output-dada2-se-unfiltered/03-alpha-diversity/evenness_group_significance.qzv",
"02-output-dada2-se-unfiltered/04-beta-diversity/bray_curtis_emperor.qzv",
"02-output-dada2-se-unfiltered/04-beta-diversity/bray_curtis_group_significance.qzv",
"02-output-dada2-se-unfiltered/04-beta-diversity/jaccard_emperor.qzv",
Expand Down Expand Up @@ -184,7 +181,6 @@ rule dada2_se_diversity_filtered:
"02-output-dada2-se-filtered/03-alpha-diversity/faith_pd_group_significance.qzv",
"02-output-dada2-se-filtered/03-alpha-diversity/observed_features_group_significance.qzv",
"02-output-dada2-se-filtered/03-alpha-diversity/shannon_group_significance.qzv",
"02-output-dada2-se-filtered/03-alpha-diversity/evenness_group_significance.qzv",
"02-output-dada2-se-filtered/04-beta-diversity/bray_curtis_emperor.qzv",
"02-output-dada2-se-filtered/04-beta-diversity/bray_curtis_group_significance.qzv",
"02-output-dada2-se-filtered/04-beta-diversity/jaccard_emperor.qzv",
Expand Down Expand Up @@ -235,7 +231,6 @@ rule deblur_se_diversity_unfiltered:
"02-output-deblur-se-unfiltered/03-alpha-diversity/faith_pd_group_significance.qzv",
"02-output-deblur-se-unfiltered/03-alpha-diversity/observed_features_group_significance.qzv",
"02-output-deblur-se-unfiltered/03-alpha-diversity/shannon_group_significance.qzv",
"02-output-deblur-se-unfiltered/03-alpha-diversity/evenness_group_significance.qzv",
"02-output-deblur-se-unfiltered/04-beta-diversity/bray_curtis_emperor.qzv",
"02-output-deblur-se-unfiltered/04-beta-diversity/bray_curtis_group_significance.qzv",
"02-output-deblur-se-unfiltered/04-beta-diversity/jaccard_emperor.qzv",
Expand Down Expand Up @@ -278,7 +273,6 @@ rule deblur_se_diversity_filtered:
"02-output-deblur-se-filtered/03-alpha-diversity/faith_pd_group_significance.qzv",
"02-output-deblur-se-filtered/03-alpha-diversity/observed_features_group_significance.qzv",
"02-output-deblur-se-filtered/03-alpha-diversity/shannon_group_significance.qzv",
"02-output-deblur-se-filtered/03-alpha-diversity/evenness_group_significance.qzv",
"02-output-deblur-se-filtered/04-beta-diversity/bray_curtis_emperor.qzv",
"02-output-deblur-se-filtered/04-beta-diversity/bray_curtis_group_significance.qzv",
"02-output-deblur-se-filtered/04-beta-diversity/jaccard_emperor.qzv",
Expand Down Expand Up @@ -1438,7 +1432,6 @@ rule generate_report_md:
vistable="02-output-{method}-{filter}/00-table-repseqs/table_summary.qzv",
vistaxbar="02-output-{method}-{filter}/01-taxonomy/taxa_barplot.qzv",
visalpharare="02-output-{method}-{filter}/03-alpha-diversity/alpha_rarefaction.qzv",
visevengs="02-output-{method}-{filter}/03-alpha-diversity/evenness_group_significance.qzv",
visfaithgs="02-output-{method}-{filter}/03-alpha-diversity/faith_pd_group_significance.qzv",
visobsfeaturesgs="02-output-{method}-{filter}/03-alpha-diversity/observed_features_group_significance.qzv",
visshannongs="02-output-{method}-{filter}/03-alpha-diversity/shannon_group_significance.qzv",
Expand Down Expand Up @@ -1613,8 +1606,6 @@ rule generate_report_md:
r"echo '' >> {output};"
r"echo '### Alpha Group Significance' >> {output};"
r"echo '' >> {output};"
r"echo Evenness QZV: [{input.visevengs}]\(../{input.visevengs}\){{target=\"_blank\"}} >> {output};"
r"echo '' >> {output};"
r"echo Faith PD QZV: [{input.visfaithgs}]\(../{input.visfaithgs}\){{target=\"_blank\"}} >> {output};"
r"echo '' >> {output};"
r"echo Observed features QZV: [{input.visobsfeaturesgs}]\(../{input.visobsfeaturesgs}\){{target=\"_blank\"}} >> {output};"
Expand Down
29 changes: 11 additions & 18 deletions notebooks/tourmaline_python_notebook.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"This Python notebook will work \"out of the box\" with the test data included with Tourmaline. To run with your own data, just make sure to change the variables in the section **Define variables** to match your metadata and desired parameters."
"This Python notebook will work \"out of the box\" with the test data included with Tourmaline. To run with your own data, make sure to change the variables in the section **File paths & variables** to match your metadata and desired parameters."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Install dependencies (first time only)"
"### Install dependencies (first time only)"
]
},
{
Expand Down Expand Up @@ -62,7 +62,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Import packages"
"### Import packages"
]
},
{
Expand All @@ -83,7 +83,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Define variables"
"### File paths & variables"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**User should change the values of `method` and `filtering` if they used a different method or filtering. Values in dict `inputs` can also be edited, e.g., changed to absolute file paths.**"
]
},
{
Expand All @@ -100,13 +107,6 @@
"factor2 = 'region'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Set file paths"
]
},
{
"cell_type": "code",
"execution_count": 4,
Expand All @@ -130,13 +130,6 @@
"}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Read and view DataFrames"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down
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