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Correct constraint doc #192

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Correct constraint doc #192

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43fb819
Merge pull request #97 from theislab/dev
davidsebfischer Aug 14, 2019
aad102e
Merge pull request #98 from theislab/dev
davidsebfischer Aug 14, 2019
062161d
Merge pull request #104 from theislab/dev
davidsebfischer Aug 21, 2019
5be8684
Merge pull request #105 from theislab/dev
davidsebfischer Aug 21, 2019
118a607
Merge pull request #106 from theislab/dev
davidsebfischer Aug 21, 2019
0249161
Merge pull request #107 from theislab/dev
davidsebfischer Aug 22, 2019
b2657b3
Merge pull request #110 from theislab/dev
davidsebfischer Aug 25, 2019
f8635bb
Merge pull request #111 from theislab/dev
davidsebfischer Aug 25, 2019
8b9ad60
Merge pull request #113 from theislab/dev
davidsebfischer Aug 26, 2019
b023a80
Fix versus_rest link
gokceneraslan Oct 7, 2019
c27eead
Remove whitespace
gokceneraslan Oct 7, 2019
dfe8304
Merge pull request #118 from gokceneraslan/patch-1
davidsebfischer Oct 8, 2019
51aaa49
Merge pull request #124 from theislab/dev
davidsebfischer Oct 31, 2019
b60bdb3
Merge branch 'dev' of https://github.com/theislab/diffxpy
davidsebfischer Feb 21, 2020
00f8a83
Merge pull request #138 from theislab/dev
davidsebfischer Feb 21, 2020
3689ea8
Merge pull request #147 from theislab/dev
davidsebfischer Mar 19, 2020
bcf8533
update constraints array doc
Hrovatin Mar 5, 2021
6ac7ac6
update constraints array doc
Hrovatin Mar 5, 2021
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56 changes: 32 additions & 24 deletions diffxpy/fit/fit.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -80,9 +80,10 @@ def model(
:param constraints_loc: Constraints for location model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -113,9 +114,10 @@ def model(
:param constraints_scale: Constraints for scale model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -289,9 +291,10 @@ def residuals(
:param constraints_loc: Constraints for location model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -322,9 +325,10 @@ def residuals(
:param constraints_scale: Constraints for scale model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -548,9 +552,10 @@ def model(
:param constraints_loc: Constraints for location model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -581,9 +586,10 @@ def model(
:param constraints_scale: Constraints for scale model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -705,9 +711,10 @@ def residuals(
:param constraints_loc: Constraints for location model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -738,9 +745,10 @@ def residuals(
:param constraints_scale: Constraints for scale model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down
42 changes: 24 additions & 18 deletions diffxpy/testing/tests.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,18 +52,20 @@ def _fit(
:param design_loc: Design matrix of location model.
:param design_loc: Design matrix of scale model.
:param constraints_loc: : Constraints for location model.
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
of that constraint (which may be dependent at an earlier constraint)
are indicated by a 1.
:param constraints_scale: : Constraints for scale model.
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -519,9 +521,10 @@ def wald(
:param constraints_loc: Constraints for location model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -552,9 +555,10 @@ def wald(
:param constraints_scale: Constraints for scale model. Can be one of the following:

- np.ndarray:
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down Expand Up @@ -1896,19 +1900,21 @@ def wald(
This makes sense for number of genes, time, pseudotime or space
for example.
:param constraints_loc: : Constraints for location model.
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
of that constraint (which may be dependent at an earlier constraint)
are indicated by a 1. It is highly recommended to only use this option
together with prebuilt design matrix for the location model, dmat_loc.
:param constraints_scale: : Constraints for scale model.
Array with constraints in rows and model parameters in columns.
Each constraint contains non-zero entries for the a of parameters that
has to sum to zero. This constraint is enforced by binding one parameter
Array with constraints in columns and model parameters in rows.
Each constraint contains non-zero entries for the constrained parameters that
have to sum to zero. For a non-constrained parameter the revelant constraint column
contains 1 in the parameter row. This constraint is enforced by binding one parameter
to the negative sum of the other parameters, effectively representing that
parameter as a function of the other parameters. This dependent
parameter is indicated by a -1 in this array, the independent parameters
Expand Down
4 changes: 1 addition & 3 deletions docs/tutorials.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -36,9 +36,7 @@ Diffxpy allows you to define a data set partition and to conduct test on each ge
Multiple tests per gene
~~~~~~~~~~~~~~~~~~~~~~~

How to perform `pairwise <https://nbviewer.jupyter.org/github/theislab/diffxpy_tutorials/tree/master/diffxpy_tutorials/test/multiple_tests_per_gene.ipynb>`__ tests.

How to perform group tests versus all other groups (versus `rest <https://nbviewer.jupyter.org/github/theislab/diffxpy_tutorials/tree/master/diffxpy_tutorials/test/multiversus_rest.ipynb>`__).
How to perform `pairwise tests, group versus rest tests and tests within each parition <https://nbviewer.jupyter.org/github/theislab/diffxpy_tutorials/tree/master/diffxpy_tutorials/test/multiple_tests_per_gene.ipynb>`__ tests.


Gene set enrichment: enrich
Expand Down