From 84431c716c208f9a78b074f8ea62d317b9c7e218 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Yoshiki=20V=C3=A1zquez=20Baeza?= Date: Fri, 3 Dec 2021 09:58:17 -0800 Subject: [PATCH] DOC: Update documentation in help text --- gemelli/_defaults.py | 9 +++++---- gemelli/q2/plugin_setup.py | 4 ++-- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/gemelli/_defaults.py b/gemelli/_defaults.py index f09efa0..caf4f27 100644 --- a/gemelli/_defaults.py +++ b/gemelli/_defaults.py @@ -26,7 +26,7 @@ DESC_ITERATIONS = ("The number of iterations to optimize the solution" " (suggested to be below 100; beware of overfitting)" " [minimum 1]") -DESC_INIT = ("The number of initialization vectors. Larger values will" +DESC_INIT = ("The number of initialization vectors. Larger values will " "give more accurate factorization but will be more " "computationally expensive [minimum 1]") DESC_ITERATIONSALS = ("Max number of Alternating Least Square (ALS)" @@ -58,11 +58,12 @@ " across which samples are paired." " At least one is required but up to four are allowed" " by other state inputs.") -QORD = ("A trajectory is an ordination that can be visualized" +QORD = ("A '%s trajectory ordination' that can be visualized " "over time or another context.") QDIST = ("A sample-sample distance matrix generated from " - " the euclidean distance of the subject-state " - "ordinations and itself.") + " the Euclidean distance of the subject-state " + "ordinations and itself. Similar to the distance matrix produced by" + " RPCA except it also accounts for the subject and state context.") QLOAD = ("Compositional biplot of subjects as points and features as arrows." " Where the variation between subject groupings is explained by the" " log-ratio between opposing arrows. " diff --git a/gemelli/q2/plugin_setup.py b/gemelli/q2/plugin_setup.py index 822f886..0ab15da 100644 --- a/gemelli/q2/plugin_setup.py +++ b/gemelli/q2/plugin_setup.py @@ -95,8 +95,8 @@ output_descriptions={'subject_biplot': QLOAD, 'state_biplot': QSOAD, 'distance_matrix': QDIST, - 'state_subject_ordination': QORD, - 'state_feature_ordination': QORD}, + 'state_subject_ordination': QORD % 'subject', + 'state_feature_ordination': QORD % 'feature'}, name='Compositional Tensor Factorization (CTF) with mode 3 tensor. This ' 'means subjects have repeated measures across only one ' 'axis (e.g. time or space).',