Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
C
cnidaria
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Aflitos, Saulo Alves
cnidaria
Commits
fe6f8c8d
Commit
fe6f8c8d
authored
8 years ago
by
Aflitos, Saulo Alves
Browse files
Options
Downloads
Patches
Plain Diff
viewer
parent
00809638
Branches
master
No related tags found
No related merge requests found
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
viewer/.gitignore
+3
-0
3 additions, 0 deletions
viewer/.gitignore
viewer/stats_to_html.py
+350
-0
350 additions, 0 deletions
viewer/stats_to_html.py
with
353 additions
and
0 deletions
viewer/.gitignore
0 → 100644
+
3
−
0
View file @
fe6f8c8d
*.html
*.css
*.js
This diff is collapsed.
Click to expand it.
viewer/stats_to_html.py
0 → 100644
+
350
−
0
View file @
fe6f8c8d
#!/usr/bin/env python
import
os
import
sys
import
argparse
from
collections
import
OrderedDict
,
defaultdict
def
sanitize
(
n
):
return
n
.
lower
().
replace
(
"
"
,
"
_
"
).
replace
(
"
.
"
,
"
_
"
)
class
table
(
object
):
def
__init__
(
self
,
lines
,
has_header
=
True
,
has_row_name
=
True
):
self
.
lines
=
lines
self
.
has_header
=
has_header
self
.
has_row_name
=
has_row_name
self
.
header
=
[]
self
.
rows
=
[]
self
.
data
=
[]
self
.
process
()
def
process
(
self
):
for
line_num
,
line
in
enumerate
(
self
.
lines
.
split
(
"
\n
"
)):
cols
=
[
l
.
strip
()
for
l
in
line
.
split
(
"
\t
"
)]
if
line_num
==
0
:
if
self
.
has_header
:
self
.
header
=
cols
elif
self
.
has_row_name
:
self
.
rows
.
append
(
cols
[
0
]
)
self
.
data
.
append
(
cols
[
1
:])
else
:
if
len
(
cols
)
>
0
and
sum
([
len
(
c
)
for
c
in
cols
])
>
0
:
self
.
data
.
append
(
cols
)
else
:
if
len
(
cols
)
>
0
and
sum
([
len
(
c
)
for
c
in
cols
])
>
0
:
if
self
.
has_row_name
:
self
.
rows
.
append
(
cols
[
0
]
)
self
.
data
.
append
(
cols
[
1
:])
else
:
self
.
data
.
append
(
cols
)
def
to_html
(
self
,
tb_id
,
tb_class
,
decimals
=
1
,
colored
=
False
,
no_diag
=
False
):
tb_class
=
sanitize
(
tb_class
)
#return OrderedDict((('header', self.header), ('rows', self.rows), ('data', self.data)))
if
no_diag
:
for
a
in
xrange
(
len
(
self
.
data
)):
self
.
data
[
a
][
a
]
=
None
min_val
=
min
([
min
([
float
(
e
)
for
e
in
d
if
e
is
not
None
])
for
d
in
self
.
data
])
max_val
=
max
([
max
([
float
(
e
)
for
e
in
d
if
e
is
not
None
])
for
d
in
self
.
data
])
print
"
min_val {} max_val {}
"
.
format
(
min_val
,
max_val
)
res
=
[
'
<table id=
"
{}
"
class=
"
table_header {}
"
min_val=
"
{}
"
max_val=
"
{}
"
>
'
.
format
(
tb_id
,
tb_class
+
(
"
colored
"
if
colored
else
""
),
min_val
,
max_val
)]
if
self
.
has_header
:
res
.
append
(
'
<tr row_num=
"
-1
"
row_name=
"
_HEADER_
"
class=
"
header_row {tb_class}_header
"
>
'
.
format
(
**
{
'
tb_class
'
:
tb_class
,
})
)
for
col_num
,
col_name
in
enumerate
(
self
.
header
):
res
.
append
(
'
<th col_num=
"
{col_num}
"
col_name=
"
{col_name}
"
class=
"
header_cell {tb_class}_header {tb_class}_th
"
><div><span>{col_name}</span></div></th>
'
.
format
(
**
{
'
col_num
'
:
col_num
,
'
col_name
'
:
col_name
,
'
tb_class
'
:
tb_class
,
})
)
res
.
append
(
'
</tr>
'
)
for
row_num
,
row
in
enumerate
(
self
.
data
):
row_name
=
row_num
if
len
(
row
)
==
0
:
continue
res
.
append
(
'
<tr row_num=
"
{row_num}
"
row_name=
"
{row_name}
"
class=
"
table_row {tb_class}_row
"
>
'
.
format
(
**
{
'
row_num
'
:
row_num
,
'
row_name
'
:
row_name
,
'
tb_class
'
:
tb_class
,
})
)
for
col_num
,
col_val
in
enumerate
(
row
):
if
self
.
has_row_name
and
col_num
==
0
:
row_name
=
self
.
rows
[
row_num
]
res
.
append
(
'
<th col_num=
"
{col_num}
"
col_name=
"
{col_name}
"
row_num=
"
{row_num}
"
row_name=
"
{row_name}
"
class=
"
row_name {tb_class}_row_name {tb_class}_th
"
>{row_name}</th>
'
.
format
(
**
{
'
col_num
'
:
col_num
,
'
col_name
'
:
self
.
header
[
col_num
],
'
row_num
'
:
row_num
,
'
row_name
'
:
row_name
,
'
tb_class
'
:
tb_class
})
)
if
self
.
has_row_name
:
col_num
+=
1
col_name
=
col_num
if
self
.
has_header
:
col_name
=
self
.
header
[
col_num
]
if
col_val
is
None
:
col_val
=
"
-
"
else
:
if
'
.
'
in
col_val
:
col_val
=
(
"
{:,.
"
+
str
(
decimals
)
+
"
f}
"
).
format
(
float
(
col_val
))
else
:
col_val
=
"
{:,d}
"
.
format
(
int
(
col_val
))
res
.
append
(
'
<td col_num=
"
{col_num}
"
col_name=
"
{col_name}
"
row_num=
"
{row_num}
"
row_name=
"
{row_name}
"
class=
"
cell {tb_class}_td
"
>{col_val}</th>
'
.
format
(
**
{
'
col_num
'
:
col_num
,
'
col_name
'
:
self
.
header
[
col_num
],
'
row_num
'
:
row_num
,
'
row_name
'
:
row_name
,
'
row_name_s
'
:
sanitize
(
row_name
)
,
'
tb_class
'
:
tb_class
,
'
col_val
'
:
col_val
})
)
res
.
append
(
'
</tr>
'
)
res
.
append
(
'
</table>
'
)
return
"
\n
"
.
join
(
res
)
def
main
():
basename
=
sys
.
argv
[
1
]
f_json
,
f_stats
,
f_count
,
f_matrix
=
[
x
.
format
(
basename
)
for
x
in
(
"
{}.json
"
,
"
{}.json.count.csv
"
,
"
{}.json.csv
"
,
"
{}.json.jaccard.matrix
"
)]
for
f
in
(
f_json
,
f_stats
,
f_count
,
f_matrix
):
if
not
os
.
path
.
exists
(
f
):
print
"
input file {} does not exists
"
.
format
(
f
)
sys
.
exit
(
1
)
json
=
open
(
f_json
,
'
r
'
).
read
()
stats
=
open
(
f_stats
,
'
r
'
).
read
()
count
=
open
(
f_count
,
'
r
'
).
read
()
matrix
=
open
(
f_matrix
,
'
r
'
).
read
()
stats_t
=
table
(
stats
,
has_header
=
True
,
has_row_name
=
True
).
to_html
(
'
stats_table
'
,
'
stats_table
'
,
decimals
=
1
,
colored
=
False
,
no_diag
=
False
)
count_t
=
table
(
count
,
has_header
=
True
,
has_row_name
=
True
).
to_html
(
'
count_table
'
,
'
count_table
'
,
decimals
=
1
,
colored
=
True
,
no_diag
=
True
)
matrix_t
=
table
(
matrix
,
has_header
=
True
,
has_row_name
=
True
).
to_html
(
'
matrix_table
'
,
'
matrix_table
'
,
decimals
=
5
,
colored
=
True
,
no_diag
=
True
)
res
=
TEMPLATE
.
format
(
**
{
"
title
"
:
basename
,
"
json
"
:
''
,
#json ,
"
count
"
:
count_t
,
"
stats
"
:
stats_t
,
"
matrix
"
:
matrix_t
,
"
script
"
:
'
<script>{}</script>
'
.
format
(
SCRIPT
),
"
css
"
:
'
<style>{}</style>
'
.
format
(
CSS
),
# "script": '<script src="{}.js"></script>'.format(basename),
# "css" : '<link rel="stylesheet" href="{}.css">'.format(basename)
})
#print res
open
(
"
{}.html
"
.
format
(
basename
),
'
w
'
).
write
(
res
)
TEMPLATE
=
"""
<!doctype html>
<html>
<head>
<meta charset=
"
UTF-8
"
>
<title>{title}</title>
{css}
<script src=
"
https://cdn.rawgit.com/gka/chroma.js/master/chroma.min.js
"
></script>
{script}
</head>
<body>
<script type=
"
application/json
"
id=
"
json
"
>
{json}
</script>
<div id=
"
stats
"
>
{stats}
</div>
<div id=
"
count
"
>
{count}
</div>
<div id=
"
matrix
"
>
{matrix}
</div>
</body>
</html>
"""
SCRIPT
=
"""
function isNumeric(n) {
//https://stackoverflow.com/questions/18082/validate-decimal-numbers-in-javascript-isnumeric
return !isNaN(parseFloat(n)) && isFinite(n);
}
var bscale = chroma.scale([
'
yellow
'
,
'
orange
'
,
'
red
'
]);
var fscale = chroma.scale([
'
black
'
,
'
white
'
]);
function heatMapColorforValue(min_val, max_val, value){
/*
2-3-4-5 = (2 - 2) / (5 - 2) = 0 / 3 = 0
2-3-4-5 = (3 - 2) / (5 - 2) = 1 / 3 = 0.3
2-3-4-5 = (4 - 2) / (5 - 2) = 2 / 3 = 0.6
2-3-4-5 = (5 - 2) / (5 - 2) = 3 / 3 = 1.0
*/
var ival = (value - min_val) / (max_val - min_val);
var bcolor = bscale(ival).hex();
var fcolor = fscale(ival).hex();
return [ival, bcolor, fcolor];
}
function color_cells() {
var coloreds = document.getElementsByClassName(
"
colored
"
);
console.log(coloreds.length, coloreds);
for (var c = 0; c < coloreds.length; c++) {
var e = coloreds[c];
var min_val = parseFloat(e.getAttribute(
'
min_val
'
));
var max_val = parseFloat(e.getAttribute(
'
max_val
'
));
console.log(
"
C
"
,c,
"
E
"
,e,
"
min
"
,min_val,
"
max
"
,max_val);
var tds = e.getElementsByTagName(
"
td
"
);
//console.log(
"
TDS
"
, tds.length, tds);
for ( var t = 0; t < tds.length; t++) {
var td = tds[t];
var value = parseFloat(td.innerHTML.replace(/,/g,
""
));
if ( isNumeric(value) ) {
var cdata = heatMapColorforValue(min_val, max_val, value);
var prop = cdata[0];
var bcolor = cdata[1];
var fcolor = cdata[2];
td.style.backgroundColor = bcolor;
//td.style.color = fcolor;
}
}
}
}
document.addEventListener(
"
DOMContentLoaded
"
, color_cells);
"""
CSS
=
"""
th.header_cell {
text-align: left;
height: 500px;
}
th.header_cell > div {
/*float: left;*/
transform:
/*translate(25px, 51px)*/
/*rotate(315deg);*/
translate(15px, 180px)
rotate(270deg);
width: 50px;
/*transform-origin: left top 0;*/
}
th.header_cell > div > span {
/*border-bottom: 1px solid #ccc;*/
padding: 5px 10px;
}
th.row_name {
text-align: left;
}
td.cell {
text-align: right;
/*text-shadow: 1px 1px 1px #000;*/
}
th {
white-space: nowrap;
}
"""
"""
<div id=
"
stats
"
>
<table id=
"
stats_table
"
class=table_header
"
stats_table
"
>
<tr row_num=
"
-1
"
row_name=
"
_HEADER_
"
class=
"
header_row stats_table_header
"
>
<th col_num=
"
0
"
col_name=
"
NAME
"
class=
"
header_cell stats_table_header stats_table_th
"
>NAME</th>
<th col_num=
"
1
"
col_name=
"
TOTAL
"
class=
"
header_cell stats_table_header stats_table_th
"
>TOTAL</th>
<th col_num=
"
2
"
col_name=
"
VALID
"
class=
"
header_cell stats_table_header stats_table_th
"
>VALID</th>
<th col_num=
"
3
"
col_name=
"
PROP
"
class=
"
header_cell stats_table_header stats_table_th
"
>PROP</th>
</tr>
<tr row_num=
"
176
"
row_name=
"
176
"
class=
"
table_row stats_table_row
"
>
<th col_num=
"
0
"
col_name=
"
NAME
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
row_name stats_table_row_name stats_table_th
"
>Tribolium castaneum</th>
<td col_num=
"
1
"
col_name=
"
TOTAL
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell stats_table_td
"
>6581748</th>
<td col_num=
"
2
"
col_name=
"
VALID
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell stats_table_td
"
>1505999</th>
<td col_num=
"
3
"
col_name=
"
PROP
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell stats_table_td
"
> 22.88</th>
</tr>
<tr row_num=
"
177
"
row_name=
"
177
"
class=
"
table_row stats_table_row
"
>
</tr>
</table>
</div>
<div id=
"
count
"
>
<table id=
"
count_table
"
class=table_header
"
count_table
"
>
<tr row_num=
"
-1
"
row_name=
"
_HEADER_
"
class=
"
header_row count_table_header
"
>
<th col_num=
"
0
"
col_name=
""
class=
"
header_cell count_table_header count_table_th
"
></th>
<th col_num=
"
1
"
col_name=
"
Arabidopsis lyrata
"
class=
"
header_cell count_table_header count_table_th
"
>Arabidopsis lyrata</th>
<th col_num=
"
2
"
col_name=
"
Arabidopsis thaliana TAIR10
"
class=
"
header_cell count_table_header count_table_th
"
>Arabidopsis thaliana TAIR10</th>
<th col_num=
"
3
"
col_name=
"
Citrus sinensis
"
class=
"
header_cell count_table_header count_table_th
"
>Citrus sinensis</th>
<th col_num=
"
176
"
col_name=
"
Struthio camelus australis
"
class=
"
header_cell count_table_header count_table_th
"
>Struthio camelus australis</th>
<th col_num=
"
177
"
col_name=
"
Tribolium castaneum
"
class=
"
header_cell count_table_header count_table_th
"
>Tribolium castaneum</th>
</tr>
<tr row_num=
"
0
"
row_name=
"
0
"
class=
"
table_row count_table_row
"
>
<th col_num=
"
0
"
col_name=
""
row_num=
"
0
"
row_name=
"
Arabidopsis lyrata
"
class=
"
row_name count_table_row_name count_table_th
"
>Arabidopsis lyrata</th>
<td col_num=
"
1
"
col_name=
"
Arabidopsis lyrata
"
row_num=
"
0
"
row_name=
"
Arabidopsis lyrata
"
class=
"
cell count_table_td
"
>0</th>
<td col_num=
"
176
"
col_name=
"
Struthio camelus australis
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell count_table_td
"
>47911</th>
<td col_num=
"
177
"
col_name=
"
Tribolium castaneum
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell count_table_td
"
>0</th>
</tr>
<tr row_num=
"
177
"
row_name=
"
177
"
class=
"
table_row count_table_row
"
>
</tr>
</table>
</div>
<div id=
"
matrix
"
>
<table id=
"
matrix_table
"
class=table_header
"
matrix_table
"
>
<tr row_num=
"
-1
"
row_name=
"
_HEADER_
"
class=
"
header_row matrix_table_header
"
>
<th col_num=
"
0
"
col_name=
""
class=
"
header_cell matrix_table_header matrix_table_th
"
></th>
<th col_num=
"
1
"
col_name=
"
Arabidopsis lyrata
"
class=
"
header_cell matrix_table_header matrix_table_th
"
>Arabidopsis lyrata</th>
<th col_num=
"
176
"
col_name=
"
Struthio camelus australis
"
class=
"
header_cell matrix_table_header matrix_table_th
"
>Struthio camelus australis</th>
<th col_num=
"
177
"
col_name=
"
Tribolium castaneum
"
class=
"
header_cell matrix_table_header matrix_table_th
"
>Tribolium castaneum</th>
<th col_num=
"
178
"
col_name=
""
class=
"
header_cell matrix_table_header matrix_table_th
"
></th>
</tr>
<tr row_num=
"
0
"
row_name=
"
0
"
class=
"
table_row matrix_table_row
"
>
<th col_num=
"
0
"
col_name=
""
row_num=
"
0
"
row_name=
"
Arabidopsis lyrata
"
class=
"
row_name matrix_table_row_name matrix_table_th
"
>Arabidopsis lyrata</th>
<td col_num=
"
1
"
col_name=
"
Arabidopsis lyrata
"
row_num=
"
0
"
row_name=
"
Arabidopsis lyrata
"
class=
"
cell matrix_table_td
"
>1.0000000000</th>
<td col_num=
"
2
"
col_name=
"
Arabidopsis thaliana TAIR10
"
row_num=
"
0
"
row_name=
"
Arabidopsis lyrata
"
class=
"
cell matrix_table_td
"
>0.7233067471</th>
<td col_num=
"
176
"
col_name=
"
Struthio camelus australis
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell matrix_table_td
"
>0.9962171649</th>
<td col_num=
"
177
"
col_name=
"
Tribolium castaneum
"
row_num=
"
176
"
row_name=
"
Tribolium castaneum
"
class=
"
cell matrix_table_td
"
>1.0000000000</th>
</tr>
<tr row_num=
"
177
"
row_name=
"
177
"
class=
"
table_row matrix_table_row
"
>
</tr>
<tr row_num=
"
178
"
row_name=
"
178
"
class=
"
table_row matrix_table_row
"
>
</tr>
</table>
</div>
"""
if
__name__
==
'
__main__
'
:
main
()
\ No newline at end of file
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment