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Development #36

Merged
merged 58 commits into from
Dec 19, 2023
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78b0b26
ms_plot
jalew188 Sep 13, 2022
fd007b1
MS_Plotter.model_mgr.transfer_learn()
jalew188 Sep 13, 2022
043096c
MS_Plotter.model_mgr.transfer_learn()
jalew188 Sep 13, 2022
10f8b98
easier access data
jalew188 Sep 13, 2022
9fa28a1
FIX plotly_hovermode
jalew188 Sep 13, 2022
a3cf678
minor updates
jalew188 Sep 14, 2022
4f8e52c
update to peptdeep latest version
jalew188 Sep 14, 2022
dbd883c
better bbplot
jalew188 Sep 15, 2022
d6812bd
reader_utils
jalew188 Sep 16, 2022
ed2eea4
Feng contrib plots
jalew188 Sep 17, 2022
8c455d8
rm alphatims version limit
jalew188 Sep 17, 2022
ec8f2b9
add_shape->update_layout
jalew188 Sep 18, 2022
e132a9e
include_precursor in xic plot
jalew188 Sep 18, 2022
3530d8a
fig.show('svg')
jalew188 Sep 18, 2022
7a8297b
refine PCC calc
jalew188 Sep 18, 2022
cb10e38
minor changes
jalew188 Sep 21, 2022
30414b2
mDIa
jalew188 Sep 25, 2022
c7d111d
integrated alpharaw
jalew188 Sep 26, 2022
1fea08e
mDIA support
jalew188 Sep 28, 2022
9fdc564
pcc
jalew188 Sep 28, 2022
eb528bc
minor update
jalew188 Sep 30, 2022
74b6798
view_dim=rt or im
jalew188 Sep 30, 2022
c441c1f
add zeros
jalew188 Oct 1, 2022
de9661f
minor updates
jalew188 Oct 4, 2022
a7facf6
tims uint16 to float
jalew188 Oct 5, 2022
fcbc6db
FIX make_subplots import
jalew188 Oct 7, 2022
bd845d2
legend_group
jalew188 Oct 7, 2022
965c099
legend_group M0 seperated
jalew188 Oct 7, 2022
2f7a044
int(charge)
jalew188 Oct 8, 2022
5655f76
FIX no peaks matched MS2
jalew188 Oct 8, 2022
4dffb59
FIX no peaks matched MS2
jalew188 Oct 8, 2022
b58e869
FIX no peaks matched MS2
jalew188 Oct 8, 2022
a83874c
FIX no peaks matched MS2
jalew188 Oct 8, 2022
b22c1f9
FIX empty matching
jalew188 Oct 9, 2022
8ef20fe
rt_tol->rt_win
jalew188 Oct 9, 2022
602c94e
minor
jalew188 Oct 12, 2022
85ed0dc
ready for PR
jalew188 Oct 27, 2022
56a1d22
find both left and left closest specs
jalew188 Oct 28, 2022
a196076
Merge pull request #32 from jalew188/peptdeep_latest
EugeniaVoytik Oct 28, 2022
14e2638
Merge branch 'peptdeep_latest' of https://github.com/mannlabs/alphavi…
jalew188 Jan 17, 2023
4b92d58
mz slicing
jalew188 Jan 17, 2023
cee7225
update ms2 plots
jalew188 Jan 17, 2023
2feb23d
frag_end_idx->frag_stop_idx; flex APIs
jalew188 Jan 19, 2023
9e4031b
rename
jalew188 Jan 19, 2023
11d56dd
use alphabase.match.match_utils instead of peptdeep's
jalew188 Jan 20, 2023
42a3f65
use ppm or not
jalew188 Feb 14, 2023
7631f51
use alpharaw.viz for thermo
zhouxiexuan Dec 19, 2023
8e78b99
add example notebook
zhouxiexuan Dec 19, 2023
59c9b83
update
zhouxiexuan Dec 19, 2023
1ca8265
peptdeep upgraded
zhouxiexuan Dec 19, 2023
32448ef
add xic plot example
zhouxiexuan Dec 19, 2023
346d736
add xic plot example
zhouxiexuan Dec 19, 2023
67a13cc
Merge pull request #35 from MannLabs/peptdeep_latest
jalew188 Dec 19, 2023
1d11c09
contrib->thermo
zhouxiexuan Dec 19, 2023
ccbe2d4
use .bumpversion.cfg
zhouxiexuan Dec 19, 2023
9b55028
move bumpversion.cfg to .bumpversion.cfg
zhouxiexuan Dec 19, 2023
fd66cf7
move .bumpversion.cfg out of misc
zhouxiexuan Dec 19, 2023
70cdeb1
Bump version: 1.1.15 → 1.2.0
zhouxiexuan Dec 19, 2023
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minor
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jalew188 committed Oct 12, 2022

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commit 602c94e73688be7dd65631a994bbdbb263cc19ec
3 changes: 0 additions & 3 deletions alphaviz/contrib/xic_plot.py
Original file line number Diff line number Diff line change
@@ -142,9 +142,6 @@ def _add_elution_profile(self,
Peptide information including sequence, fragment patterns, rt,
and im values.

rt_tol: float
The rt tolerance value. Default: 30 ppm.

im_tol: float
The im tolerance value. Default: 0.05 ppm.