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grlloydgrlloyd
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update 'type' and matching 'value' for prototype entity objects
1 parent d1477b9 commit 384d31b

16 files changed

+47
-31
lines changed

‎R/HSDEM_class.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@ HSDEM<-setClass(
3838
params.mtc=entity.stato(name='Multiple Test Correction method',
3939
stato.id='OBI:0200089',
4040
value='none',
41-
type='numeric',
41+
type='character',
4242
description='The method used to adjust for multiple comparisons.'
4343
),
4444

‎R/HSD_class.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ HSD<-setClass(
4343
params.mtc=entity.stato(name='Multiple Test Correction method',
4444
stato.id='OBI:0200089',
4545
value='none',
46-
type='numeric',
46+
type='character',
4747
description='The method used to adjust for multiple comparisons.'
4848
),
4949
params.unbalanced=entity(name='Unbalanced model',

‎R/PCA_plotfcns.R‎

Lines changed: 9 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,8 @@ pca_correlation_plot<-setClass(
2020
params.components=entity(name='Components to plot',
2121
value=c(1,2),
2222
type='numeric',
23-
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.'
23+
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.',
24+
max_length=2
2425
)
2526

2627
)
@@ -79,7 +80,8 @@ pca_scores_plot<-setClass(
7980
params.components=entity(name='Components to plot',
8081
value=c(1,2),
8182
type='numeric',
82-
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.'
83+
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.',
84+
max_length=2
8385
),
8486

8587
params.points_to_label=enum(name='points_to_label',
@@ -244,8 +246,9 @@ pca_biplot_plot<-setClass(
244246
params.components=entity(name='Components to plot',
245247
value=c(1,2),
246248
type='numeric',
247-
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.'
248-
),
249+
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.',
250+
max_length=2
251+
),
249252
params.points_to_label=entity(name='points_to_label',
250253
value='none',
251254
type='character',
@@ -380,7 +383,8 @@ pca_loadings_plot<-setClass(
380383
params.components=entity(name='Components to plot',
381384
value=c(1,2),
382385
type='numeric',
383-
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.'
386+
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.',
387+
max_length=2
384388
),
385389
params.style=enum(name='Plot style',
386390
value='points',

‎R/PLSDA_charts.R‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,8 @@ plsda_scores_plot<-setClass(
2424
params.components=entity(name='Components to plot',
2525
value=c(1,2),
2626
type='numeric',
27-
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.'
27+
description='the components to be plotted e.g. c(1,2) plots component 1 on the x axis and component 2 on the y axis.',
28+
max_length=2
2829
),
2930
params.points_to_label=entity(name='points_to_label',
3031
value='none',

‎R/anova_class.R‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ ANOVA<-setClass(
4848
params.mtc=entity.stato(name='Multiple Test Correction method',
4949
stato.id='OBI:0200089',
5050
value='fdr',
51-
type='numeric',
51+
type='character',
5252
description='The method used to adjust for multiple comparisons.'
5353
),
5454
params.type=enum(name='ANOVA type',
@@ -60,17 +60,20 @@ ANOVA<-setClass(
6060
outputs.f_statistic=entity.stato(name='F-statistic',
6161
stato.id='STATO:0000176',
6262
type='numeric',
63-
description='the value of the calculated statistic which is converted to a p-value when compared to an F-distribution.'
63+
description='the value of the calculated statistic which is converted to a p-value when compared to an F-distribution.',
64+
value=numeric(0)
6465
),
6566
outputs.p_value=entity.stato(name='p value',
6667
stato.id='STATO:0000175',
6768
type='numeric',
68-
description='the probability of observing the calculated t-statistic.'
69+
description='the probability of observing the calculated t-statistic.',
70+
value=numeric(0)
6971
),
7072
outputs.significant=entity(name='Significant features',
7173
#stato.id='STATO:0000069',
7274
type='logical',
73-
description='TRUE if the calculated p-value is less than the supplied threhold (alpha)'
75+
description='TRUE if the calculated p-value is less than the supplied threhold (alpha)',
76+
value=logical(0)
7477
)
7578
)
7679
)

‎R/blank_filter_class.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ blank_filter<-setClass(
6767
value='V1'),
6868
params.fraction=entity(name='Fraction in blank',
6969
description='Remove features only if they occur in a sufficient proportion of the blanks',
70-
type='character',
70+
type='numeric',
7171
value=0)
7272
)
7373
)

‎R/classical_lsq_class.R‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -61,21 +61,24 @@ classical_lsq<-setClass(
6161
params.mtc=entity.stato(name='Multiple testing Correction method',
6262
stato.id='OBI:0200089',
6363
value='fdr',
64-
type='numeric',
64+
type='character',
6565
description='The method used to adjust for multiple comparisons.'
6666
),
6767
outputs.coefficients=entity(name='Regression coefficients',
6868
type='numeric',
69-
description='The regression coefficients for each model.'
69+
description='The regression coefficients for each model.',
70+
value=numeric(0)
7071
),
7172
outputs.p_value=entity.stato(name='p value',
7273
stato.id='STATO:0000175',
7374
type='numeric',
74-
description='the probability of observing the calculated t-statistic.'
75+
description='the probability of observing the calculated t-statistic.',
76+
value=numeric(0)
7577
),
7678
outputs.significant=entity(name='Significant features',
7779
type='logical',
78-
description='TRUE if the calculated p-value is less than the supplied threhold (alpha)'
80+
description='TRUE if the calculated p-value is less than the supplied threhold (alpha)',
81+
value=logical(0)
7982
)
8083
)
8184
)

‎R/confounders_clsq_class.R‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -47,7 +47,7 @@ confounders_clsq<-setClass(
4747
predicted='p_value',
4848

4949
params.threshold=entity(name='Confounding factor threshold',
50-
type='character',
50+
type='numeric',
5151
description='threshold for accepting a factor as confounding (0 < threshold < 1)',
5252
value=0.15
5353
),
@@ -71,7 +71,7 @@ confounders_clsq<-setClass(
7171
params.mtc=entity.stato(name='Multiple testing Correction method',
7272
stato.id='OBI:0200089',
7373
value='fdr',
74-
type='numeric',
74+
type='character',
7575
description='The method used to adjust for multiple comparisons.'
7676
)
7777
)
@@ -189,7 +189,7 @@ confounders_lsq.barchart<-setClass(
189189
type="barchart",
190190
params.feature_to_plot=entity(name='Feature to plot',
191191
value=1,
192-
type='character_or_numeric',
192+
type='numeric',
193193
description='The name of the feature to be plotted.'
194194
),
195195
params.threshold=entity(name='Threshold',

‎R/dataset_chart_classes.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -474,7 +474,7 @@ dataset.boxplot<-setClass(
474474
),
475475
params.number=entity(name='Number of features/samples',
476476
value=50,
477-
type='logical',
477+
type='numeric',
478478
description='The number of features/samples to plot.'
479479
)
480480
)

‎R/fisher_exact_class.R‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ fisher_exact<-setClass(
5454
params.mtc=entity.stato(name='Multiple Test Correction method',
5555
stato.id='OBI:0200089',
5656
value='fdr',
57-
type='numeric',
57+
type='character',
5858
description='The method used to adjust for multiple comparisons.'
5959
),
6060
params.factor_name=entity(name='Factor name',
@@ -70,7 +70,8 @@ fisher_exact<-setClass(
7070
outputs.p_value=entity.stato(name='p value',
7171
stato.id='STATO:0000175',
7272
type='numeric',
73-
description='the probability of observing the calculated t-statistic.'
73+
description='the probability of observing the calculated t-statistic.',
74+
value=-1
7475
),
7576
outputs.significant=entity(name='Significant features',
7677
#stato.id='STATO:0000069',

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