From a5d6bc17d429d02eceb9073fbf5457ecb369d01c Mon Sep 17 00:00:00 2001 From: SabrinaRichter Date: Mon, 31 Oct 2022 14:57:20 +0100 Subject: [PATCH 1/3] removed stuff that is messing with my plots --- sceptre/sceptre.py | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/sceptre/sceptre.py b/sceptre/sceptre.py index 2a68f72..aa0ebbb 100644 --- a/sceptre/sceptre.py +++ b/sceptre/sceptre.py @@ -15,34 +15,6 @@ import seaborn as sns import warnings -# output scanpy logs -logging.basicConfig(level=logging.INFO) -sc.settings.verbosity = 3 -# don´t show this numpy warning -warnings.filterwarnings("ignore", message="All-NaN slice encountered") - -# basic plotting settings -plt.rcParams["xtick.labelsize"] = 8 -plt.rcParams["ytick.labelsize"] = 8 -plt.rcParams["font.size"] = 8 -plt.rcParams["font.family"] = "sans-serif" -plt.rcParams["font.sans-serif"] = "Arial" -plt.rcParams["figure.figsize"] = 7.2, 4.45 -plt.rcParams["figure.titlesize"] = 9 -plt.rcParams["figure.dpi"] = 120 -plt.rcParams["axes.titlesize"] = 9 -plt.rcParams["axes.labelsize"] = 8 -plt.rcParams["axes.axisbelow"] = True -plt.rcParams["axes.linewidth"] = 0.5 -plt.rcParams["lines.linewidth"] = 0.7 -plt.rcParams["lines.markersize"] = 2 -plt.rcParams["legend.fontsize"] = 8 -plt.rcParams["boxplot.flierprops.marker"] = "." -plt.rcParams["boxplot.flierprops.markerfacecolor"] = "k" -plt.rcParams["boxplot.flierprops.markersize"] = 2 -plt.rcParams["pdf.fonttype"] = 42 # to make pdf text available for illustrator -plt.rcParams["ps.fonttype"] = 42 # to make pdf text available for illustrator - figwd = 7.2 # standard figure width cellsize = 20 # size to plot cells wspace = 1 # space between scanpy plots to make room for legends From 9e82dbae3230ce63b5ee2c930023430fd78617f0 Mon Sep 17 00:00:00 2001 From: SabrinaRichter Date: Mon, 31 Oct 2022 15:09:57 +0100 Subject: [PATCH 2/3] also imputing nan values --- sceptre/sceptre.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/sceptre/sceptre.py b/sceptre/sceptre.py index aa0ebbb..24ec58a 100644 --- a/sceptre/sceptre.py +++ b/sceptre/sceptre.py @@ -1063,16 +1063,20 @@ def impute(adata: AnnData, **kwargs): Updates `adata` with the imputed expression values. """ - if 0 in adata.X: - from sklearn.impute import KNNImputer - - imputer = KNNImputer(missing_values=0, **kwargs) - if (adata.X == 0).all(axis=0).any(): - print("remove all-zero proteins:") - sc.pp.filter_genes(adata, min_cells=1) - adata.X = imputer.fit_transform(adata.X) + if np.isnan(adata.X).any(): + missing_values = np.nan + elif 0 in adata.X: + missing_values = 0 else: warnings.warn("No zeros in adata") + return + + from sklearn.impute import KNNImputer + imputer = KNNImputer(missing_values=missing_values, **kwargs) + sc.pp.filter_genes(adata, min_cells=1) + adata.X = imputer.fit_transform(adata.X) + + def find_embedding_params( From a2d4f9ab7259c1fa6d450a744a72a05d62aad062 Mon Sep 17 00:00:00 2001 From: SabrinaRichter Date: Wed, 2 Nov 2022 10:50:29 +0100 Subject: [PATCH 3/3] allowed for non unique FileID + Channel combinations --- sceptre/sceptre.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/sceptre/sceptre.py b/sceptre/sceptre.py index 24ec58a..3495ac1 100644 --- a/sceptre/sceptre.py +++ b/sceptre/sceptre.py @@ -540,7 +540,8 @@ def normalize( quant = pd.DataFrame( adata.X.T.copy(), columns=adata.obs[["File ID", "Channel"]] - .set_index(["File ID", "Channel"]) + .reset_index() + .set_index(["index", "File ID", "Channel"]) .index, ).replace(0, np.nan) @@ -554,7 +555,7 @@ def normalize( med_tot = med.median(axis=1) factors = med.divide(med_tot, axis=0) - quant = quant.groupby(axis=1, level=0).apply( + quant = quant.groupby(axis=1, level="File ID", group_keys=False).apply( lambda x: x.divide(factors.loc[:, x.name], axis=0) ) @@ -565,7 +566,7 @@ def normalize( med_tot = med.median(axis=1) factors = med.divide(med_tot, axis=0) - quant = quant.groupby(axis=1, level=1).apply( + quant = quant.groupby(axis=1, level="Channel", group_keys=False).apply( lambda x: x.divide(factors.loc[:, x.name], axis=0) ) @@ -583,7 +584,7 @@ def normalize( med_tot = med.median(axis=1) factors = med.divide(med_tot, axis=0) - quant = quant.groupby(axis=1, level=0).apply( + quant = quant.groupby(axis=1, level="File ID", group_keys=False).apply( lambda x: x.divide(factors.loc[:, x.name], axis=0) ) @@ -596,7 +597,7 @@ def normalize( med_tot = med.median(axis=1) factors = med.divide(med_tot, axis=0) - quant = quant.groupby(axis=1, level=1).apply( + quant = quant.groupby(axis=1, level="Channel", group_keys=False).apply( lambda x: x.divide(factors.loc[:, x.name], axis=0) )