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Hoogenboom
fdstools
Commits
670d34f9
Commit
670d34f9
authored
Dec 07, 2018
by
Hoogenboom, Jerry
Browse files
Add Samplevis option to apply graph filtering before noise correction
parent
13451a12
Changes
3
Hide whitespace changes
Inline
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README.rst
View file @
670d34f9
...
...
@@ -29,6 +29,9 @@ Alternatively, FDSTools can be installed by running:
FDSTools Changelog
------------------
v1.1.2
- Includes Samplevis v2.2.1
v1.1.1
- Includes TSSV v1.1.1
...
...
@@ -616,6 +619,10 @@ v1.0.0
Samplevis
~~~~~~~~~
v2.2.1
- Added an option to apply graph filtering before noise correction (on by
default)
v2.2.0
- Fixed incorrect calculation of 'percentage of highest' if the 'sequence'
with the highest read count within a marker is the aggregated 'Other
...
...
fdstools/vis/samplevis/index.html
View file @
670d34f9
...
...
@@ -24,7 +24,7 @@
<meta
charset=
"UTF-8"
>
<meta
name=
"viewport"
content=
"width=device-width, initial-scale=1"
>
<title>
Sample Visualisation - FDSTools
</title>
<!-- VERSION 2.
1.2
-->
<!-- VERSION 2.
2.1
-->
<!-- BEGIN_LIBRARIES -->
<script
src=
"https://vega.github.io/vega-editor/vendor/d3.min.js"
></script>
<script
src=
"https://vega.github.io/vega/vega.min.js"
></script>
...
...
@@ -531,6 +531,14 @@
</label>
</td>
</tr>
<tr>
<td
colspan=
"2"
>
<label>
<input
type=
"checkbox"
id=
"filteruncorrected"
checked
>
Filter before noise correction
</label>
</td>
</tr>
<tr>
<td
colspan=
"2"
>
<label>
...
...
@@ -1667,6 +1675,9 @@ function onLoadSpec(has_data, no_file_chooser){
document
.
getElementById
(
"
shownegative
"
).
addEventListener
(
'
change
'
,
function
(){
setSignalValue
(
"
show_negative
"
,
this
.
checked
);
},
false
);
document
.
getElementById
(
"
filteruncorrected
"
).
addEventListener
(
'
change
'
,
function
(){
setSignalValue
(
"
filter_uncorrected
"
,
this
.
checked
);
},
false
);
document
.
getElementById
(
"
showother
"
).
addEventListener
(
'
change
'
,
function
(){
setSignalValue
(
"
show_other
"
,
this
.
checked
);
},
false
);
...
...
@@ -1701,6 +1712,7 @@ function onLoadSpec(has_data, no_file_chooser){
document
.
getElementById
(
"
minOa
"
).
value
=
getSignalValue
(
"
allele_orientation_threshold
"
);
document
.
getElementById
(
"
minBias
"
).
value
=
getSignalValue
(
"
bias_threshold
"
);
document
.
getElementById
(
"
shownegative
"
).
checked
=
getSignalValue
(
"
show_negative
"
);
document
.
getElementById
(
"
filteruncorrected
"
).
checked
=
getSignalValue
(
"
filter_uncorrected
"
);
document
.
getElementById
(
"
showother
"
).
checked
=
getSignalValue
(
"
show_other
"
);
document
.
getElementById
(
"
sortstrbylength
"
).
checked
=
getSignalValue
(
"
sort_str_by_length
"
);
document
.
getElementById
(
"
commonrange
"
).
checked
=
(
graph_spec
.
marks
[
1
].
scales
[
0
].
domain
.
data
==
"
table
"
);
...
...
fdstools/vis/samplevis/samplevis.json
View file @
670d34f9
{
"fdstools_visversion"
:
"2.2.
0
"
,
"fdstools_visversion"
:
"2.2.
1
"
,
"width"
:
600
,
"height"
:
10
,
"signals"
:
[
...
...
@@ -47,6 +47,10 @@
"name"
:
"show_negative"
,
"init"
:
true
},
{
"name"
:
"filter_uncorrected"
,
"init"
:
true
},
{
"name"
:
"show_other"
,
"init"
:
true
...
...
@@ -181,7 +185,7 @@
{
"type"
:
"aggregate"
,
"groupby"
:
[
"marker"
],
"summarize"
:
{
"total_added"
:
[
"max"
]}
"summarize"
:
{
"total_added"
:
[
"max"
],
"total"
:
[
"max"
]}
}
]
},
...
...
@@ -196,7 +200,7 @@
{
"type"
:
"aggregate"
,
"groupby"
:
[
"marker"
],
"summarize"
:
{
"total_added"
:
[
"sum"
]}
"summarize"
:
{
"total_added"
:
[
"sum"
],
"total"
:
[
"sum"
]}
}
]
},
...
...
@@ -230,6 +234,16 @@
"field"
:
"pct_of_sum"
,
"expr"
:
"datum.aggrs.sum_total_added? (datum.total_added / datum.aggrs.sum_total_added * 100) : 100"
},
{
"type"
:
"formula"
,
"field"
:
"pct_of_max_uncorrected"
,
"expr"
:
"datum.aggrm.max_total? (datum.total / datum.aggrm.max_total * 100) : 100"
},
{
"type"
:
"formula"
,
"field"
:
"pct_of_sum_uncorrected"
,
"expr"
:
"datum.aggrs.sum_total? (datum.total / datum.aggrs.sum_total * 100) : 100"
},
{
"type"
:
"formula"
,
"field"
:
"strlength"
,
...
...
@@ -316,7 +330,7 @@
{
"type"
:
"formula"
,
"field"
:
"sequence"
,
"expr"
:
"((show_negative? abs(
datum.total_added) : datum.total_added) >= amplitude_threshold && (show_negative? abs(datum.pct_of_max) : datum.pct_of_max) >= amplitude_pct_threshold && (show_negative? abs(datum.pct_of_sum) : datum.pct_of_sum) >= amplitude_markerpct_threshold && min(show_negative? abs(datum.forward_added) : datum.forward_added, show_negative? abs(datum.reverse_added)
: datum.reverse_added) >= orientation_threshold)? datum.sequence : 'Other sequences'"
"expr"
:
"((show_negative? abs(
filter_uncorrected? datum.total : datum.total_added) : filter_uncorrected? datum.total : datum.total_added) >= amplitude_threshold && (show_negative? abs(filter_uncorrected? datum.pct_of_max_uncorrected : datum.pct_of_max) : filter_uncorrected? datum.pct_of_max_uncorrected : datum.pct_of_max) >= amplitude_pct_threshold && (show_negative? abs(filter_uncorrected? datum.pct_of_sum_uncorrected : datum.pct_of_sum) : filter_uncorrected? datum.pct_of_sum_uncorrected : datum.pct_of_sum) >= amplitude_markerpct_threshold && min(show_negative? abs(filter_uncorrected? datum.forward : datum.forward_added) : filter_uncorrected? datum.forward : datum.forward_added, show_negative? abs(filter_uncorrected? datum.reverse : datum.reverse_added) : filter_uncorrected? datum.reverse
: datum.reverse_added) >= orientation_threshold)? datum.sequence : 'Other sequences'"
},
{
"type"
:
"filter"
,
...
...
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