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My branch #21

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5e96797
Ridgelines
KristianBoje Jan 19, 2023
d9d4556
Update Kristian_rewrite_for_streamlit.py
KristianBoje Jan 19, 2023
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14 changes: 2 additions & 12 deletions Kristian_rewrite_for_streamlit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@ def common_type_gen(fragments_dataframe):
common_type = common_type.replace("n", "not annotated", regex=True)
common_type = common_type.replace("t-","",regex=True)
common_type = common_type.replace("-t","",regex=True)
#counts = common_type.value_counts()
fragments_dataframe['frag_types'] = common_type
return common_type

Expand All @@ -34,20 +33,18 @@ def common_type_gen(fragments_dataframe):
def common_type_hist(common_type):
fig = go.Figure([go.Histogram(x=common_type)])
return fig
#fig.show()


def common_type_pie(common_type):
counts = common_type.value_counts()
fig = go.Figure([go.Pie(labels=counts.keys(), values=counts)])
return fig
#fig.show()

# intensity distribution of different ions
# density or probability
def log_ion_intens_dist(fragments_dataframe):
histnorm = "probability"
types = fragments_dataframe["frag_types"].unique()
#print(types)
histograms = list()
for t in types:
histograms.append(go.Histogram(x=np.log(fragments_dataframe[fragments_dataframe.frag_types == t].frag_intensity),histnorm=histnorm, name=t, nbinsx=50))
Expand Down Expand Up @@ -79,7 +76,6 @@ def log_ion_intens_ridge(fragments_dataframe):
def rel_ion_intens_perc(fragments_dataframe):
histnorm = "probability"
types = fragments_dataframe["frag_types"].unique()
#print(types)
histograms = list()
for t in types:
histograms.append(go.Histogram(x=fragments_dataframe[fragments_dataframe.frag_types == t].perc_of_total_intensity,histnorm=histnorm, name=t, nbinsx=50))
Expand All @@ -89,7 +85,6 @@ def rel_ion_intens_perc(fragments_dataframe):
title="Histograms of relative intensities per ion type",
xaxis_title="intensity",
yaxis_title=histnorm)
#fig.show()
return fig

### Ridgelines of relative intensities per ion type
Expand All @@ -107,12 +102,12 @@ def rel_ion_intens_ridge(fragments_dataframe):
yaxis_title=histnorm)
return fig

#new comment
# relative intensity to total intensity distribution of different ions
# density or probability
def rel_ion_intens_prop(fragments_dataframe):
histnorm = "probability"
types = fragments_dataframe["frag_types"].unique()
#print(types)
histograms = list()
for t in types:
histograms.append(go.Histogram(x=fragments_dataframe[fragments_dataframe.frag_types == t].prop_intensity_to_base_peak,histnorm=histnorm, name=t, nbinsx=50))
Expand All @@ -122,7 +117,6 @@ def rel_ion_intens_prop(fragments_dataframe):
title="Histograms of relative intensities to base peak per ion type",
xaxis_title="Percentage per base peak",
yaxis_title=histnorm)
#fig.show()
return fig

## Ridgelines of relative intensities to base peak per ion type
Expand All @@ -145,7 +139,6 @@ def rel_ion_intens_prop_ridge(fragments_dataframe):
def mz_dist_ion_type(fragments_dataframe):
histnorm = "probability"
types = fragments_dataframe["frag_types"].unique()
#print(types)
histograms = list()
for t in types:
histograms.append(go.Histogram(x=fragments_dataframe[fragments_dataframe.frag_types == t].frag_mz, histnorm=histnorm, name=t, nbinsx=50))
Expand All @@ -155,7 +148,6 @@ def mz_dist_ion_type(fragments_dataframe):
title="Histograms of mz values per ion type",
xaxis_title="mz",
yaxis_title=histnorm)
#fig.show()
return fig


Expand All @@ -174,7 +166,6 @@ def per_spec_ion_type(spectra_dataframe):
title="Histograms of percentages of ion type per spectrum",
xaxis_title="Percentage",
yaxis_title=histnorm)
#fig.show()
return fig

### Same for intensities
Expand All @@ -190,7 +181,6 @@ def per_spec_ion_intens(spectra_dataframe):
title="Histograms of percentages of ion type per spectrum",
xaxis_title="Percentage",
yaxis_title=histnorm)
#fig.show()
return fig

## Distribution of total intensity of single amino acids
Expand Down