Merge pull request #46 from sbslee/1.15.0-dev

1.15.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,6 +1,13 @@
 Changelog
 *********
 
+1.15.0 (2022-08-23)
+-------------------
+
+* Update :meth:`pname` method to support taxa names that don't have a delimiter such as ASV IDs (e.g. ``1ad289cd8f44e109fd95de0382c5b252``). Basically, the method will simply return the input name as is.
+* Add new argument ``delimiter`` to :meth:`pname` method.
+* Add new method :meth:`group_correlation_heatmap`.
+
 1.14.0 (2022-06-24)
 -------------------
 

README.rst

@@ -28,17 +28,21 @@ and the GitHub repository (https://github.com/sbslee/dokdo). If applicable,
 please also consider citing the following preprint in which Dokdo was first
 described:
 
-JY Park, H Yoon, S Lee, et al. Do Different Samples From Pregnant Women and
-Their Neonates Share the Common Microbiome: A Prospective Cohort Study.
-November 29th, 2021. Research Square.
-doi: https://doi.org/10.21203/rs.3.rs-1062191/v1.
+- JY Park, H Yoon, S Lee, et al. `Do Different Samples From Pregnant Women and Their Neonates Share the Common Microbiome: A Prospective Cohort Study <https://doi.org/10.21203/rs.3.rs-1062191/v1>`__. Research Square. November 29th, 2021.
 
 Below is an incomplete list of publications which have used Dokdo:
 
+- `Hsieh et al., 2022 <https://doi.org/10.1038/s41598-022-13289-9>`__ in *Scientific Reports*: Gut microbiome profiles and associated metabolic pathways in patients of adult-onset immunodeficiency with anti-interferon-gamma autoantibodies.
+- `Reinold et al., 2022 <https://www.frontiersin.org/articles/10.3389/fcimb.2022.848650/full>`__ in *Frontiers in Cellular and Infection Microbiology*: The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients.
 - `Silva de Carvalho et al., 2022 <https://www.sciencedirect.com/science/article/pii/S0889159121006127>`__ in *Brain, Behavior, and Immunity*: Post-ischemic protein restriction induces sustained neuroprotection, neurological recovery, brain remodeling, and gut microbiota rebalancing.
 - `Park et al., 2021 <https://www.nature.com/articles/s41598-021-95789-8>`__ in *Scientific Reports*: Effect of black ginseng and silkworm supplementation on obesity, the transcriptome, and the gut microbiome of diet-induced overweight dogs.
 - `Reinold et al., 2021 <https://www.frontiersin.org/articles/10.3389/fcimb.2021.747816/full>`__ in *Frontiers in Cellular and Infection Microbiology*: A Pro-Inflammatory Gut Microbiome Characterizes SARS-CoV-2 Infected Patients and a Reduction in the Connectivity of an Anti-Inflammatory Bacterial Network Associates With Severe COVID-19.
 
+Support Dokdo
+=============
+
+If you find my work useful, please consider becoming a `sponsor <https://github.com/sponsors/sbslee>`__.
+
 CLI Examples
 ============
 

data/moving-pictures-tutorial/table-l6.qza

@@ -0,0 +1,50 @@
+sample_name	barcode	mouse_id	genotype	cage_id	donor	donor_status	days_post_transplant	genotype_and_donor_status
+#q2:types		categorical	categorical	categorical	categorical	categorical	numeric	categorical
+recip.220.WT.OB1.D7	CCTCCGTCATGG	457	wild type	C35	hc_1	Healthy	49	wild type and Healthy
+recip.290.ASO.OB2.D1	AACAGTAAACAA	456	susceptible	C35	hc_1	Healthy	49	susceptible and Healthy
+recip.389.WT.HC2.D21	ATGTATCAATTA	435	susceptible	C31	hc_1	Healthy	21	susceptible and Healthy
+recip.391.ASO.PD2.D14	GTCAGTATGGCT	435	susceptible	C31	hc_1	Healthy	14	susceptible and Healthy
+recip.391.ASO.PD2.D21	AGACAGTAGGAG	437	susceptible	C31	hc_1	Healthy	21	susceptible and Healthy
+recip.391.ASO.PD2.D7	GGTCTTAGCACC	435	susceptible	C31	hc_1	Healthy	7	susceptible and Healthy
+recip.400.ASO.HC2.D14	CGTTCGCTAGCC	437	susceptible	C31	hc_1	Healthy	14	susceptible and Healthy
+recip.401.ASO.HC2.D7	ATTTACAATTGA	437	susceptible	C31	hc_1	Healthy	7	susceptible and Healthy
+recip.403.ASO.PD2.D21	CGCAGATTAGTA	456	susceptible	C35	hc_1	Healthy	21	susceptible and Healthy
+recip.411.ASO.HC2.D14	ATGTTAGGGAAT	456	susceptible	C35	hc_1	Healthy	14	susceptible and Healthy
+recip.411.ASO.HC2.D21	CTCATATGCTAT	457	wild type	C35	hc_1	Healthy	21	wild type and Healthy
+recip.411.ASO.HC2.D49	GCAACGAACGAG	435	susceptible	C31	hc_1	Healthy	49	susceptible and Healthy
+recip.412.ASO.HC2.D14	AAGTGGCTATCC	457	wild type	C35	hc_1	Healthy	14	wild type and Healthy
+recip.412.ASO.HC2.D7	GCATTCGGCGTT	456	susceptible	C35	hc_1	Healthy	7	susceptible and Healthy
+recip.413.WT.HC2.D7	ACCAGTGACTCA	457	wild type	C35	hc_1	Healthy	7	wild type and Healthy
+recip.456.ASO.HC3.D49	ACGGCGTTATGT	468	wild type	C42	hc_1	Healthy	49	wild type and Healthy
+recip.458.ASO.HC3.D21	ACGGCCCTGGAG	468	wild type	C42	hc_1	Healthy	21	wild type and Healthy
+recip.458.ASO.HC3.D49	CATTTGACGACG	469	wild type	C42	hc_1	Healthy	49	wild type and Healthy
+recip.459.WT.HC3.D14	ACATGGGCGGAA	468	wild type	C42	hc_1	Healthy	14	wild type and Healthy
+recip.459.WT.HC3.D21	CATAAATTCTTG	469	wild type	C42	hc_1	Healthy	21	wild type and Healthy
+recip.459.WT.HC3.D49	GCTGCGTATACC	536	susceptible	C43	pd_1	PD	49	susceptible and PD
+recip.460.WT.HC3.D14	CTGCGGATATAC	469	wild type	C42	hc_1	Healthy	14	wild type and Healthy
+recip.460.WT.HC3.D21	GTCAATTAGTGG	536	susceptible	C43	pd_1	PD	21	susceptible and PD
+recip.460.WT.HC3.D49	GAGAAGCTTATA	537	wild type	C43	pd_1	PD	49	wild type and PD
+recip.460.WT.HC3.D7	GACCCGTTTCGC	468	wild type	C42	hc_1	Healthy	7	wild type and Healthy
+recip.461.ASO.HC3.D21	AGCCCGCAAAGG	537	wild type	C43	pd_1	PD	21	wild type and PD
+recip.461.ASO.HC3.D49	GGCGTAACGGCA	538	wild type	C44	pd_1	PD	49	wild type and PD
+recip.461.ASO.HC3.D7	ATTGCCTTGATT	469	wild type	C42	hc_1	Healthy	7	wild type and Healthy
+recip.462.WT.PD3.D14	GTGAGGGCAAGT	536	susceptible	C43	pd_1	PD	14	susceptible and PD
+recip.462.WT.PD3.D21	GGCCTATAAGTC	538	wild type	C44	pd_1	PD	21	wild type and PD
+recip.462.WT.PD3.D49	AATACAGACCTG	539	susceptible	C44	pd_1	PD	49	susceptible and PD
+recip.462.WT.PD3.D7	TTAGGATTCTAT	536	susceptible	C43	pd_1	PD	7	susceptible and PD
+recip.463.WT.PD3.D14	ATATTGGCAGCC	537	wild type	C43	pd_1	PD	14	wild type and PD
+recip.463.WT.PD3.D21	CGCGGCGCAGCT	539	susceptible	C44	pd_1	PD	21	susceptible and PD
+recip.463.WT.PD3.D7	GTTTATCTTAAG	537	wild type	C43	pd_1	PD	7	wild type and PD
+recip.464.WT.PD3.D14	TCATCCGTCGGC	538	wild type	C44	pd_1	PD	14	wild type and PD
+recip.465.ASO.PD3.D14	GGCTTCGGAGCG	539	susceptible	C44	pd_1	PD	14	susceptible and PD
+recip.465.ASO.PD3.D7	CAGTCTAGTACG	538	wild type	C44	pd_1	PD	7	wild type and PD
+recip.466.ASO.PD3.D7	GTGGGACTGCGC	539	susceptible	C44	pd_1	PD	7	susceptible and PD
+recip.467.WT.HC3.D49.a	GTCAGGTGCGGC	437	susceptible	C31	hc_1	Healthy	49	susceptible and Healthy
+recip.467.WT.HC3.D49.b	GTTAACTTACTA	546	susceptible	C49	pd_1	PD	49	susceptible and PD
+recip.536.ASO.PD4.D49	CAAATTCGGGAT	547	wild type	C49	pd_1	PD	49	wild type and PD
+recip.537.WT.PD4.D21	CTCTATTCCACC	546	susceptible	C49	pd_1	PD	21	susceptible and PD
+recip.538.WT.PD4.D21	ATGGATAGCTAA	547	wild type	C49	pd_1	PD	21	wild type and PD
+recip.539.ASO.PD4.D14	GATCCGGCAGGA	546	susceptible	C49	pd_1	PD	14	susceptible and PD
+recip.539.ASO.PD4.D7	GTTCGAGTGAAT	546	susceptible	C49	pd_1	PD	7	susceptible and PD
+recip.540.ASO.HC4.D14	CTTCCAACTCAT	547	wild type	C49	pd_1	PD	14	wild type and PD
+recip.540.ASO.HC4.D7	CGGCCTAAGTTC	547	wild type	C49	pd_1	PD	7	wild type and PD

data/parkinsons-mouse-tutorial/dada2_table.qza

@@ -458,6 +458,13 @@ heatmap
 
 .. autofunction:: heatmap
 
+group_correlation_heatmap
+-------------------------
+
+.. currentmodule:: dokdo.api.cross_association
+
+.. autofunction:: group_correlation_heatmap
+
 Other Plotting Methods
 ======================
 

data/parkinsons-mouse-tutorial/dada2_table_l6.qza

@@ -15,7 +15,9 @@
 from .distance_matrix_plot import distance_matrix_plot
 from .taxa_abundance import taxa_abundance_bar_plot, taxa_abundance_box_plot
 from .ancom_volcano_plot import ancom_volcano_plot
-from .cross_association import cross_association_table, cross_association_heatmap, cross_association_regplot
+from .cross_association import (cross_association_table,
+    cross_association_heatmap, cross_association_regplot,
+    group_correlation_heatmap)
 
 from .addsig import addsig
 from .addpairs import addpairs
@@ -31,4 +33,5 @@
            'taxa_abundance_bar_plot', 'taxa_abundance_box_plot',
            'ancom_volcano_plot', 'cross_association_table',
            'cross_association_heatmap', 'cross_association_regplot',
-           'addsig', 'regplot', 'addbiplot', 'ordinate', 'pname', 'get_mf']
+           'group_correlation_heatmap', 'addsig', 'regplot', 'addbiplot',
+           'ordinate', 'pname', 'get_mf']