def recolor(self):
dataset = self.data
try:
colormap = cm.get_cmap(self.config.spectracmap, dataset.len)
except:
print("Failed to get spectra cmap", self.config)
colormap = cm.get_cmap('rainbow', dataset.len)
peakcolors = colormap(np.arange(dataset.len))
colors = peakcolors
for i in range(0, dataset.len):
s = dataset.spectra[i]
index = int(s.index)
# print(s.index, s.var1)
if colors is not None:
color = wx.Colour(int(round(colors[i][0] * 255)),
int(round(colors[i][1] * 255)),
int(round(colors[i][2] * 255)),
alpha=255)
self.SetItemBackgroundColour(index, col=color)
luminance = ud.get_luminance(color, type=2)
# print(wx.Colour(colout), luminance)
if luminance < luminance_cutoff:
self.SetItemTextColour(index, col=white_text)
else:
self.SetItemTextColour(index, col=black_text)
s.color = colors[i]
self.colors = colors
def populate(self, pks):
self.ClearGrid()
l = len(pks.peaks)
collabels = [
"Mass", "Intensity", "DScore", "Uniqueness/Fit", "Peak Shape",
"Charge Dist.", "FWHM Penalties",
"Limited Score (DScore without CSScore)"
]
cl = len(collabels)
self.CreateGrid(l + 1, cl)
w = 120
for i, c in enumerate(collabels):
self.SetCellValue(0, i, c)
self.SetColSize(i, width=w)
self.SetCellFont(
0, i,
wx.Font(10, wx.FONTFAMILY_DEFAULT, wx.FONTSTYLE_NORMAL,
wx.FONTWEIGHT_BOLD))
self.SetColSize(0, width=75)
self.SetColSize(1, width=75)
colormap = cm.get_cmap('RdYlGn')
norm = Normalize(vmin=0, vmax=1)
for index, p in enumerate(pks.peaks):
i = index + 1
self.SetCellValue(i, 0, str(p.mass))
self.SetCellFont(
i, 0,
wx.Font(10, wx.FONTFAMILY_DEFAULT, wx.FONTSTYLE_NORMAL,
wx.FONTWEIGHT_BOLD))
self.SetCellValue(i, 1, str(p.height))
scores = [
p.dscore, p.uscore, p.mscore, p.cs_score, p.fscore, p.lscore
]
scores = deepcopy(scores)
cindex = 2
for s in scores:
self.SetCellValue(i, cindex, scr(s))
color = colormap(norm(s))
color = wx.Colour(int(round(color[0] * 255)),
int(round(color[1] * 255)),
int(round(color[2] * 255)),
alpha=255)
self.SetCellBackgroundColour(i, cindex, color)
luminance = ud.get_luminance(color, type=2)
if luminance < luminance_cutoff:
self.SetCellTextColour(i, cindex, white_text)
else:
self.SetCellTextColour(i, cindex, black_text)
cindex += 1
def on_popup_five(self, event=None):
"""
Spawns a dialog for the first selected item to select the color.
Redraws the list control with the new colors and then triggers an EVT_DELETE_SELECTION_2.
:param event: Unused Event
:return: None
"""
# Change Color
item = self.list_ctrl.GetFirstSelected()
col = self.list_ctrl.GetItemBackgroundColour(item)
print("Color In:", col)
col = wx.Colour(int(col[0]),
int(col[1]),
int(col[2]),
alpha=int(col.alpha))
col2 = wx.ColourData()
col2.SetColour(col)
colout = col2
dlg = wx.ColourDialog(None, data=col2)
if dlg.ShowModal() == wx.ID_OK:
coloutdlg = dlg.GetColourData()
colout = deepcopy(coloutdlg.GetColour())
print("Color Out", colout)
dlg.Destroy()
else:
dlg.Destroy()
return
topcolor = ([colout[0] / 255., colout[1] / 255., colout[2] / 255.])
self.list_ctrl.SetItemBackgroundColour(item, col=colout)
luminance = ud.get_luminance(wx.Colour(colout), type=2)
#print(wx.Colour(colout), luminance)
if luminance < luminance_cutoff:
self.list_ctrl.SetItemTextColour(item, col=white_text)
else:
self.list_ctrl.SetItemTextColour(item, col=black_text)
peak = tofloat(self.list_ctrl.GetItem(item, col=1).GetText())
i = ud.nearest(self.pks.masses, peak)
self.pks.peaks[i].color = topcolor
num = self.list_ctrl.GetSelectedItemCount()
for i in range(1, num):
item = self.list_ctrl.GetNextSelected(item)
self.list_ctrl.SetItemBackgroundColour(item, col=colout)
if luminance < luminance_cutoff:
self.list_ctrl.SetItemTextColour(item, col=white_text)
else:
self.list_ctrl.SetItemTextColour(item, col=black_text)
peak = tofloat(self.list_ctrl.GetItem(item, col=1).GetText())
i = ud.nearest(self.pks.masses, peak)
self.pks.peaks[i].color = topcolor
newevent = wx.PyCommandEvent(self.EVT_DELETE_SELECTION_2._getEvtType(),
self.GetId())
self.GetEventHandler().ProcessEvent(newevent)
def populate(self, dataset, colors=None):
self.DeleteAllItems()
try:
colormap = cm.get_cmap(self.config.spectracmap, dataset.len)
except:
print("Failed to get spectra cmap", self.config)
colormap = cm.get_cmap('rainbow', dataset.len)
peakcolors = colormap(np.arange(dataset.len))
if colors is None:
colors = peakcolors
for i in range(0, dataset.len):
s = dataset.spectra[i]
index = self.InsertItem(dataset.len, str(s.index))
try:
self.SetItem(index, 1, str(s.var1))
except:
self.SetItem(index, 1, str(i))
try:
self.SetItem(index, 2, str(s.var2))
except:
self.SetItem(index, 2, str(0))
try:
self.SetItem(index, 3, s.name)
except:
self.SetItem(index, 3, "")
self.SetItemData(index, i)
if colors is not None:
color = wx.Colour(int(round(colors[i][0] * 255)),
int(round(colors[i][1] * 255)),
int(round(colors[i][2] * 255)),
alpha=255)
self.SetItemBackgroundColour(index, col=color)
luminance = ud.get_luminance(color, type=2)
# print(wx.Colour(colout), luminance)
if luminance < luminance_cutoff:
self.SetItemTextColour(index, col=white_text)
else:
self.SetItemTextColour(index, col=black_text)
s.color = colors[i]
self.data = dataset
self.colors = colors
self.rename_column(1, dataset.v1name)
self.rename_column(2, dataset.v2name)
self.freeze_reorder = False
def on_popup_seven(self, event=None):
"""
Spawns a dialog for the first selected item to select the color.
Redraws the list control with the new colors and then triggers an EVT_DELETE_SELECTION_2.
:param event: Unused Event
:return: None
"""
# Change Color
item = self.list.GetFirstSelected()
col = self.list.GetItemBackgroundColour(item)
print("Color In:", col)
col = wx.Colour(int(col[0]),
int(col[1]),
int(col[2]),
alpha=int(col.alpha))
col2 = wx.ColourData()
col2.SetColour(col)
colout = col2
dlg = wx.ColourDialog(None, data=col2)
if dlg.ShowModal() == wx.ID_OK:
colout = dlg.GetColourData()
colout = deepcopy(colout.GetColour())
print("Color Out", colout)
dlg.Destroy()
self.list.SetItemBackgroundColour(item, col=colout)
colout = colout.Get(includeAlpha=True)
luminance = ud.get_luminance(wx.Colour(colout), type=2)
colout = ([
colout[0] / 255., colout[1] / 255., colout[2] / 255.,
colout[3] / 255.
])
if luminance < luminance_cutoff:
self.list.SetItemTextColour(item, col=white_text)
else:
self.list.SetItemTextColour(item, col=black_text)
self.pres.on_color_change(item, colout)
def add_data(self, pks, show="area", collab1="Mass (Da)"):
"""
Add data from a Peaks object to the list_ctrl
:param pks: Peaks object
:param show: Keyword describing what to show in column 1
area = p.area
integral = p.integral
diff = p.diff
:param collab1: Column 1 label
:return: None
"""
self.list_ctrl.DeleteAllItems()
self.pks = pks
col = self.list_ctrl.GetColumn(3)
if not self.meta:
col.SetText("Area")
if show == "avgcharge":
col.SetText("Avg. Charge")
if "score" in show:
col.SetText("DScore")
self.list_ctrl.SetColumn(3, col)
self.list_ctrl.SetColumnWidth(3, 65)
try:
col = self.list_ctrl.GetColumn(1)
col.SetText(collab1)
self.list_ctrl.SetColumn(1, col)
self.list_ctrl.SetColumnWidth(1, -2)
except Exception as e:
pass
for i in range(0, self.pks.plen):
p = pks.peaks[i]
self.list_ctrl.InsertItem(i, p.textmarker)
# self.list_ctrl.SetItem(i, 1, str(p.mass))
if p.mass == round(p.mass):
p.mass = int(p.mass)
self.list_ctrl.SetItem(i, 1, f'{p.mass:,}')
else:
self.list_ctrl.SetItem(i, 1, f'{float(str(p.mass)):,}')
self.list_ctrl.SetItem(i, 2, "%.2f" % p.height)
try:
if show == "area":
self.list_ctrl.SetItem(i, 3, str(p.area))
elif show == "integral":
self.list_ctrl.SetItem(i, 3, "%.2f" % p.integral)
elif show == "diff":
self.list_ctrl.SetItem(i, 3, str(p.diff))
elif show == "avgcharge":
self.list_ctrl.SetItem(i, 3, str(p.avgcharge))
elif show == "mscore":
self.list_ctrl.SetItem(i, 3,
str(np.round(p.mscore * 100, 2)))
elif show == "dscore":
self.list_ctrl.SetItem(i, 3,
str(np.round(p.dscore * 100, 2)))
else:
self.list_ctrl.SetItem(i, 3, "")
except (ValueError, AttributeError, TypeError):
self.list_ctrl.SetItem(i, 3, "")
self.list_ctrl.SetItem(i, 4, str(p.label))
self.list_ctrl.SetItemData(i, i)
color = wx.Colour(int(round(p.color[0] * 255)),
int(round(p.color[1] * 255)),
int(round(p.color[2] * 255)),
alpha=255)
self.list_ctrl.SetItemBackgroundColour(i, col=color)
# textcolor = wx.Colour(255 - color.Red(), 255 - color.Green(), 255-color.Blue()) #Inverted. Looks bad.
luminance = ud.get_luminance(color, type=2)
#print(color, luminance)
if luminance < luminance_cutoff:
self.list_ctrl.SetItemTextColour(i, col=white_text)
self.remove = []
listmix.ColumnSorterMixin.__init__(self, 4)
def score_plots2(eng, save=False):
import matplotlib.pyplot as plt
from matplotlib import rcParams
rcParams['ps.useafm'] = True
rcParams['ps.fonttype'] = 42
rcParams['pdf.fonttype'] = 42
colormap = cm.get_cmap('RdYlGn')
norm = Normalize(vmin=0, vmax=1)
plt.rcParams.update({'font.size': 10})
fig = plt.figure(figsize=[4, 3])
p1 = plt.subplot(211)
plt.plot(eng.data.data2[:, 0], eng.data.data2[:, 1] * 100, color="k")
plt.xlabel("$\it{m/z}$")
p1.get_yaxis().set_ticks([0, 50, 100])
p1.get_yaxis().set_ticklabels(["0", '%', "100"])
p1.spines['top'].set_visible(False)
p1.spines['right'].set_visible(False)
plt.ylim(0, 100)
plt.xlim(np.amin(eng.data.data2[:, 0]), np.amax(eng.data.data2[:, 0]))
p2 = plt.subplot(212)
plt.plot(eng.data.massdat[:, 0] / 1000., eng.data.massdat[:, 1], color="k")
plt.xlabel("Mass (kDa)")
p2.get_yaxis().set_ticks([0, 50, 100])
p2.get_yaxis().set_ticklabels(["0", '%', "100"])
p2.spines['top'].set_visible(False)
p2.spines['right'].set_visible(False)
plt.ylim(0, 100)
xmin = np.amin(eng.data.massdat[:, 0]) / 1000
xmax = np.amax(eng.data.massdat[:, 0]) / 1000
plt.xlim(xmin, xmax)
offset = 0.2 * np.amax(eng.data.massdat[:, 1])
for k, p in enumerate(eng.pks.peaks):
text = str(int(round(p.dscore * 100)))
color = colormap(norm(p.dscore))
lum = ud.get_luminance(color)
if lum > luminance_cutoff / 255.:
#print(p.mass, lum, color)
color = np.array(color) * 0.8
color[3] = 1
p2.text(p.mass / 1000.,
p.height + offset,
text,
horizontalalignment="center",
verticalalignment="top",
color=color)
pass
text = "UniScore=" + str(int(round(eng.pks.uniscore * 100)))
color = colormap(norm(eng.pks.uniscore))
p2.text(xmax,
100,
text,
horizontalalignment="right",
verticalalignment="top",
color=color)
plt.tight_layout()
if save:
fig.savefig("Fig1.pdf")
fig.savefig("Fig1.png")
# plt.show()
return fig