From 1097ca8602c199abcecf8ee8ba563b6b2137a65f Mon Sep 17 00:00:00 2001
From: Roel van Esch <roel.vanesch@wur.nl>
Date: Wed, 14 Dec 2022 05:18:29 +0100
Subject: [PATCH] Figure and table paths adjusted for new directory layout
---
docs/source/tutorial/tutorial_part2.rst | 2 +-
docs/source/tutorial/tutorial_part4.rst | 4 ++--
docs/source/tutorial/tutorial_part5.rst | 12 ++++++------
docs/source/user_guide/characterize.rst | 10 +++++-----
docs/source/user_guide/construct.rst | 8 ++++----
docs/source/user_guide/differences.rst | 12 ++++++------
docs/source/user_guide/phylogeny.rst | 4 ++--
7 files changed, 26 insertions(+), 26 deletions(-)
diff --git a/docs/source/tutorial/tutorial_part2.rst b/docs/source/tutorial/tutorial_part2.rst
index 47103b27a..9c34fca4d 100644
--- a/docs/source/tutorial/tutorial_part2.rst
+++ b/docs/source/tutorial/tutorial_part2.rst
@@ -5,7 +5,7 @@ To demonstrate the main functionalities of PanTools we use a small
chloroplasts dataset to avoid long construction times.
.. csv-table::
- :file: tables/chloroplast_datasets.csv
+ :file: ../tables/chloroplast_datasets.csv
:header-rows: 1
:delim: ;
diff --git a/docs/source/tutorial/tutorial_part4.rst b/docs/source/tutorial/tutorial_part4.rst
index 6c03bf9d0..fae3ffe3d 100644
--- a/docs/source/tutorial/tutorial_part4.rst
+++ b/docs/source/tutorial/tutorial_part4.rst
@@ -25,7 +25,7 @@ Input data
----------
.. csv-table::
- :file: tables/bacteria_datasets.csv
+ :file: ../tables/bacteria_datasets.csv
:header-rows: 1
:delim: ;
@@ -123,7 +123,7 @@ core, accessory or unique part of the pangenome.
$ pantools gene_classification pecto_dickeya_DB
-.. figure:: figures/classify_table.png
+.. figure:: ../figures/classify_table.png
:width: 600
:align: center
diff --git a/docs/source/tutorial/tutorial_part5.rst b/docs/source/tutorial/tutorial_part5.rst
index dba729db0..cff012a33 100644
--- a/docs/source/tutorial/tutorial_part5.rst
+++ b/docs/source/tutorial/tutorial_part5.rst
@@ -188,7 +188,7 @@ Go to https://itol.embl.de and click on “Upload a tree” under the
**tree text:** textbox or can click the button to upload the .newick
file.
-.. figure:: figures/tutorial_phylogeny1.png
+.. figure:: ../figures/tutorial_phylogeny1.png
:width: 600
:align: center
@@ -206,7 +206,7 @@ Basic controls ITOL
This enables you to visualize the values as text or symbol on the
branch. or by coloring the branch or adjusting the width.
-.. figure:: figures/tutorial_phylogeny2.png
+.. figure:: ../figures/tutorial_phylogeny2.png
:width: 600
:align: center
@@ -215,7 +215,7 @@ Basic controls ITOL
click it so a pop-up menu appears. Click “tree structure” followed by
“Reroot the tree here”.
-.. figure:: figures/tutorial_phylogeny3.png
+.. figure:: ../figures/tutorial_phylogeny3.png
:width: 600
:align: center
@@ -248,7 +248,7 @@ Copy the two low_temperature.txt files from the label/strain_name/ and
ring/strain_name/ directories to your personal computer. Click and move
the ring template file into the tree visualization webpage.
-.. figure:: figures/tutorial_phylogeny4.png
+.. figure:: ../figures/tutorial_phylogeny4.png
:width: 600
:align: center
@@ -256,7 +256,7 @@ The resulting tree should look this when: the tree is rooted with the
*Dickeya* genome, bootstrap values are displayed as text and the ring
color template was included.
-.. figure:: figures/tutorial_phylogeny_color.png
+.. figure:: ../figures/tutorial_phylogeny_color.png
:width: 600
:align: center
@@ -264,7 +264,7 @@ Tree coloring is especially useful for large datasets. An example is
shown in the figure below, where members of the same species share a
color.
-.. figure:: figures/tutorial_phylogeny_tree.png
+.. figure:: ../figures/tutorial_phylogeny_tree.png
:width: 600
:align: center
diff --git a/docs/source/user_guide/characterize.rst b/docs/source/user_guide/characterize.rst
index 9c13d9150..b1e277bb7 100644
--- a/docs/source/user_guide/characterize.rst
+++ b/docs/source/user_guide/characterize.rst
@@ -19,7 +19,7 @@ categories can be assigned:
.. _classify table:
-.. figure:: figures/classify_table.png
+.. figure:: ../figures/classify_table.png
:width: 600
:align: center
@@ -274,7 +274,7 @@ database.
- **core_unique_thresholds.R**, the R script plots the number of
(soft) core unique/cloud homology groups for all tested thresholds.
-.. figure:: figures/core_unique_thresholds.png
+.. figure:: ../figures/core_unique_thresholds.png
:width: 600
:align: center
@@ -437,7 +437,7 @@ Output files for homology-group based estimation are written to
average and median group gain and loss between pangenome sizes.
- **heaps_law.R**, an R script to perform Heaps' law.
-.. figure:: figures/size.png
+.. figure:: ../figures/size.png
:width: 600
:align: center
@@ -696,7 +696,7 @@ with the frequency of per genome and.
- **cog_per_class.R**, an R script to plot the distribution of COG
categories over the core, accessory, unique homology groups.
-.. figure:: figures/COG_abundance.png
+.. figure:: ../figures/COG_abundance.png
:width: 600
:align: center
@@ -829,7 +829,7 @@ Additional files are generated per individual genome and placed in
- **mol_function.pdf**, dot visualisation of the Molecular Function GO
hierarchy.
-.. figure:: figures/bio_process.png
+.. figure:: ../figures/bio_process.png
:width: 600
:align: center
diff --git a/docs/source/user_guide/construct.rst b/docs/source/user_guide/construct.rst
index 598e8d31b..85fd2a28f 100644
--- a/docs/source/user_guide/construct.rst
+++ b/docs/source/user_guide/construct.rst
@@ -229,7 +229,7 @@ setting can be seen in the table below. We recommend using the
sub-parameters.
.. csv-table::
- :file: tables/relaxation.csv
+ :file: ../tables/relaxation.csv
:header-rows: 1
:delim: ;
@@ -346,7 +346,7 @@ that are present in all genomes are used to validate each setting.
F-score &= 2 \frac{Recall * Precision}{Recall + Precision}
-.. figure:: figures/true_false_positives.png
+.. figure:: ../figures/true_false_positives.png
:width: 600
:align: center
@@ -454,7 +454,7 @@ database.
homology groups the BUSCO genes were placed for the different
groupings.
-.. figure:: figures/best_grouping.png
+.. figure:: ../figures/best_grouping.png
:width: 300
:align: center
@@ -830,7 +830,7 @@ The first time running this function .INFO files are combined into a new
file **COMBINATION_INFO_FILES** and removed afterwards.
.. csv-table::
- :file: tables/functional_databases.csv
+ :file: ../tables/functional_databases.csv
:header-rows: 1
:delim: ;
diff --git a/docs/source/user_guide/differences.rst b/docs/source/user_guide/differences.rst
index 0445b539e..870501a85 100644
--- a/docs/source/user_guide/differences.rst
+++ b/docs/source/user_guide/differences.rst
@@ -19,14 +19,14 @@ into homology groups which serve as main input for many functionalities.
In addition to the single layer in panproteomes and three layers in
pangenomes, a functional layer can be included in both databases. This
-layer consists of multiple functional annotation databases (e.g. GO,
+layer consists of multiple functional annotation databases (e.g. GO,
PFAM) and connects proteins with a shared function.
Since there is only a protein layer and functional layer present in
panproteomes, not all functions can be utilized. See the table below for
which functions can be used for pangenomes and panproteomes.
-.. figure:: figures/layers.png
+.. figure:: ../figures/layers.png
:width: 600
:align: center
@@ -39,28 +39,28 @@ Available functions
:doc:`construct`
.. csv-table::
- :file: tables/differences_construct.csv
+ :file: ../tables/differences_construct.csv
:header-rows: 1
:delim: ;
:doc:`characterize`
.. csv-table::
- :file: tables/differences_characterize.csv
+ :file: ../tables/differences_characterize.csv
:header-rows: 1
:delim: ;
:doc:`explore`
.. csv-table::
- :file: tables/differences_explore.csv
+ :file: ../tables/differences_explore.csv
:header-rows: 1
:delim: ;
:doc:`phylogeny`
.. csv-table::
- :file: tables/differences_phylogeny.csv
+ :file: ../tables/differences_phylogeny.csv
:header-rows: 1
:delim: ;
diff --git a/docs/source/user_guide/phylogeny.rst b/docs/source/user_guide/phylogeny.rst
index 32fab5f47..fa0820d7e 100644
--- a/docs/source/user_guide/phylogeny.rst
+++ b/docs/source/user_guide/phylogeny.rst
@@ -768,11 +768,11 @@ There is a maximum of 20 possible colors that are used in the following
order:
.. csv-table::
- :file: tables/colors.csv
+ :file: ../tables/colors.csv
:header-rows: 1
:delim: ;
-.. figure:: figures/color_templates.png
+.. figure:: ../figures/color_templates.png
:width: 600
:align: center
--
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