+
+
+ Source code for PyWGCNA.comparison
import math
@@ -133,8 +142,10 @@ Source code for PyWGCNA.comparison
UNDERLINE = "\033[4m"
-[docs]class Comparison:
- """
+
+[docs]
+class Comparison:
+ """
A class used to compare PyWGCNA to another PyWGCNA or any gene marker table
:param geneModules: gene modules of networks
@@ -155,8 +166,10 @@ Source code for PyWGCNA.comparison
self.P_value = None
self.fraction = None
-[docs] def calculateJaccardSimilarity(self):
- """
+
+[docs]
+ def calculateJaccardSimilarity(self):
+ """
Calculate jaccard similarity matrix along multiple networks
:return: dataframe containing jaccard similarity between all modules in all PyWGCNA objects
@@ -193,8 +206,11 @@ Source code for PyWGCNA.comparison
return jaccard_similarity
-[docs] def calculateFraction(self):
- """
+
+
+[docs]
+ def calculateFraction(self):
+ """
Calculate common fraction along multiple networks
:return: dataframe containing fraction between all modules in all netwroks
@@ -230,8 +246,11 @@ Source code for PyWGCNA.comparison
return fraction
-[docs] def calculatePvalue(self):
- """
+
+
+[docs]
+ def calculatePvalue(self):
+ """
Calculate pvalue of fraction along multiple networks
:return: dataframe containing pvalue between all modules in all netwroks
@@ -275,15 +294,21 @@ Source code for PyWGCNA.comparison
return pvalue
-[docs] def compareNetworks(self):
- """
+
+
+[docs]
+ def compareNetworks(self):
+ """
compare Networks
"""
self.calculateJaccardSimilarity()
self.calculateFraction()
self.calculatePvalue()
-[docs] def plotHeatmapComparison(self,
+
+
+[docs]
+ def plotHeatmapComparison(self,
color="jaccard_similarity",
row_cluster=True,
col_cluster=True,
@@ -291,7 +316,7 @@ Source code for PyWGCNA.comparison
plot_show=True,
plot_format="pdf",
file_name="heatmap_comparison"):
- """
+ """
plot heatmap comparison
:param color: how to color heatmap (options: jaccard_similarity or fraction) default: jaccard_similarity
@@ -347,7 +372,10 @@ Source code for PyWGCNA.comparison
else:
plt.close()
-[docs] def plotJaccardSimilarity(self,
+
+
+[docs]
+ def plotJaccardSimilarity(self,
color=None,
cutoff=0.1,
figsize=None,
@@ -355,7 +383,7 @@ Source code for PyWGCNA.comparison
plot_show=True,
plot_format="png",
file_name="jaccard_similarity"):
- """
+ """
Plot jaccard similarity matrix as a network
:param color: if you want to color nodes for each networks separately
@@ -433,7 +461,10 @@ Source code for PyWGCNA.comparison
else:
plt.close()
-[docs] def plotBubbleComparison(self,
+
+
+[docs]
+ def plotBubbleComparison(self,
bubble_size="jaccard_similarity",
cutoff=0.01,
color=None,
@@ -444,7 +475,7 @@ Source code for PyWGCNA.comparison
plot_show=True,
plot_format="png",
file_name="bubble_comparison"):
- """
+ """
plot comparison matrix as a bubble plot
:param bubble_size: which information you want to use for size of bubble (options: jaccard_similarity or fraction) default: jaccard_similarity
@@ -484,7 +515,7 @@ Source code for PyWGCNA.comparison
elif bubble_size == "fraction":
size = self.fraction.copy(deep=True)
else:
- sys.exit("Color is not correct!")
+ sys.exit(f"bubble_size={bubble_size} is not correct!")
np.fill_diagonal(size.values, 0)
P_value[size == 0] = np.nan
@@ -524,6 +555,10 @@ Source code for PyWGCNA.comparison
sm = plt.cm.ScalarMappable(cmap="viridis", norm=norm)
sm.set_array([])
+ # Remove the legend and add a colorbar
+ ax.get_legend().remove()
+ fig.colorbar(sm, shrink=0.25, label='-log10(P_value)', ax=ax)
+
fig.canvas.draw()
if color is not None:
@@ -546,24 +581,26 @@ Source code for PyWGCNA.comparison
ax.set_xlabel('')
ax.set_ylabel('')
- # Remove the legend and add a colorbar
- ax.get_legend().remove()
- ax.figure.colorbar(sm, shrink=0.25, label='-log10(P_value)')
+ if bubble_size == "jaccard_similarity":
+ legend_title = "Jaccard Index"
+ elif bubble_size == "fraction":
+ legend_title = "Fraction"
handles, labels = ax.get_legend_handles_labels()
entries_to_skip = labels.index('size') + 1
handles = handles[entries_to_skip:]
labels = labels[entries_to_skip:]
- for h in handles[1:]:
- sizes = [s for s in h.get_sizes()]
- h.set_sizes(sizes)
+ #for h in handles[1:]:
+ # sizes = [s for s in h.get_sizes()]
+ # h.set_sizes(sizes)
labels = labels[:1] + [f'{float(lab):.2f}' for lab in labels[1:]]
legend_size = ax.legend(handles, labels,
- title=bubble_size,
- bbox_to_anchor=(1.04, 1),
+ title=legend_title,
+ bbox_to_anchor=(1, 1),
loc=2,
borderaxespad=0.,
- frameon=False)
+ frameon=False,
+ title_fontsize=15)
plt.gca().add_artist(legend_size)
legend_elements = []
@@ -573,11 +610,12 @@ Source code for PyWGCNA.comparison
legend_elements.append(tmp)
ax.legend(handles=legend_elements,
- title='networks',
+ title='Networks',
bbox_to_anchor=(1.04, 0),
loc=3,
borderaxespad=0.,
- frameon=False)
+ frameon=False,
+ title_fontsize=15)
if save:
plt.savefig(f"{file_name}.{plot_format}")
@@ -586,9 +624,12 @@ Source code for PyWGCNA.comparison
else:
plt.close()
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def jaccard(list1, list2):
- """
+ """
Calculate jaccard similarity matrix for two lists
:param list1: first list containing the data
@@ -603,8 +644,11 @@ Source code for PyWGCNA.comparison
union = (len(list1) + len(list2)) - intersection
return float(intersection) / union
-[docs] def saveComparison(self, name="comparison"):
- """
+
+
+[docs]
+ def saveComparison(self, name="comparison"):
+ """
save comparison object as comparison.p near to the script
:param name: name of the pickle file (default: comparison.p)
@@ -615,7 +659,9 @@ Source code for PyWGCNA.comparison
picklefile = open(f"{name}.p", 'wb')
pickle.dump(self, picklefile)
- picklefile.close()
+ picklefile.close()
+
+
@@ -630,7 +676,7 @@ Source code for PyWGCNA.comparison
diff --git a/docs/html/_modules/PyWGCNA/geneExp.html b/docs/html/_modules/PyWGCNA/geneExp.html
index 9137c88c..1f1c2dcd 100644
--- a/docs/html/_modules/PyWGCNA/geneExp.html
+++ b/docs/html/_modules/PyWGCNA/geneExp.html
@@ -1,18 +1,16 @@
-
+
PyWGCNA.geneExp — PyWGCNA documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -102,7 +100,18 @@
-
+
+
+
+
Source code for PyWGCNA.geneExp
import numpy as np
@@ -115,8 +124,10 @@ Source code for PyWGCNA.geneExp
np.seterr(divide='ignore', invalid='ignore')
-[docs]class GeneExp:
- """
+
+[docs]
+class GeneExp:
+ """
A class used to creat gene expression anndata along data trait including both genes and samples information.
:param species: species of the data you use i.e mouse, human
@@ -175,9 +186,11 @@ Source code for PyWGCNA.geneExp
self.geneExpr = ad.AnnData(X=expressionList, obs=sampleInfo, var=geneInfo)
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def updateGeneInfo(geneExpr, geneInfo=None, path=None, sep=','):
- """
+ """
add/update genes info in expr anndata
:param geneExpr: gene expression data along with sample and genes/transcript information
@@ -208,9 +221,12 @@ Source code for PyWGCNA.geneExp
return geneExpr
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def updateSampleInfo(geneExpr, sampleInfo=None, path=None, sep=','):
- """
+ """
add/update metadata in expr anndata
:param geneExpr: gene expression data along with sample and genes/transcript information
@@ -239,7 +255,9 @@ Source code for PyWGCNA.geneExp
geneExpr.obs.drop(same_columns, axis=1, inplace=True)
geneExpr.obs = pd.concat([geneExpr.obs, sampleInfo], axis=1).loc[geneExpr.obs.index, :]
- return geneExpr
+ return geneExpr
+
+
@@ -254,7 +272,7 @@ Source code for PyWGCNA.geneExp
diff --git a/docs/html/_modules/PyWGCNA/utils.html b/docs/html/_modules/PyWGCNA/utils.html
index 162c2d35..3841e1a8 100644
--- a/docs/html/_modules/PyWGCNA/utils.html
+++ b/docs/html/_modules/PyWGCNA/utils.html
@@ -1,18 +1,16 @@
-
+
PyWGCNA.utils — PyWGCNA documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -102,7 +100,18 @@
-
+
+
+
+
Source code for PyWGCNA.utils
import pickle
@@ -128,8 +137,10 @@ Source code for PyWGCNA.utils
# read WGCNA obj
-[docs]def readWGCNA(file):
- """
+
+[docs]
+def readWGCNA(file):
+ """
Read a WGCNA from a saved pickle file.
:param file: Name / path of WGCNA object
@@ -148,9 +159,12 @@ Source code for PyWGCNA.utils
return wgcna
+
# compare serveral networks
-[docs]def compareNetworks(PyWGCNAs):
- """
+
+[docs]
+def compareNetworks(PyWGCNAs):
+ """
Compare serveral PyWGCNA objects
:param PyWGCNAs: list of PyWGCNA objects
@@ -168,9 +182,12 @@ Source code for PyWGCNA.utils
return compare
+
# compare WGCNA to single cell
-[docs]def compareSingleCell(PyWGCNAs, sc):
- """
+
+[docs]
+def compareSingleCell(PyWGCNAs, sc):
+ """
Compare WGCNA and gene marker from single cell experiment
:param PyWGCNAs: WGCNA object
@@ -192,11 +209,14 @@ Source code for PyWGCNA.utils
return compare
-[docs]def getGeneList(dataset='mmusculus_gene_ensembl',
+
+
+[docs]
+def getGeneList(dataset='mmusculus_gene_ensembl',
attributes=['ensembl_gene_id', 'external_gene_name', 'gene_biotype'],
maps=['gene_id', 'gene_name', 'go_id'],
server_domain="http://ensembl.org/biomart"):
- """
+ """
get table that map gene ensembl id to gene name from biomart
:param dataset: name of the dataset we used from biomart; mouse: mmusculus_gene_ensembl and human: hsapiens_gene_ensembl
@@ -246,11 +266,14 @@ Source code for PyWGCNA.utils
return geneInfo
-[docs]def getGeneListGOid(dataset='mmusculus_gene_ensembl',
+
+
+[docs]
+def getGeneListGOid(dataset='mmusculus_gene_ensembl',
attributes=['ensembl_gene_id', 'external_gene_name', 'go_id'],
Goid='GO:0003700',
server_domain="http://ensembl.org/biomart"):
- """
+ """
get table that find gene id and gene name to specific Go term from biomart
:param dataset: name of the dataset we used from biomart; mouse: mmusculus_gene_ensembl and human: hsapiens_gene_ensembl
@@ -300,9 +323,12 @@ Source code for PyWGCNA.utils
return geneInfo
+
# read comparison obj
-[docs]def readComparison(file):
- """
+
+[docs]
+def readComparison(file):
+ """
Read a comparison from a saved pickle file.
:param file: Name / path of comparison object
@@ -319,6 +345,7 @@ Source code for PyWGCNA.utils
print(f"{BOLD}{OKBLUE}Reading comparison done!{ENDC}")
return comparison
+
@@ -333,7 +360,7 @@ Source code for PyWGCNA.utils
diff --git a/docs/html/_modules/PyWGCNA/wgcna.html b/docs/html/_modules/PyWGCNA/wgcna.html
index 04729b4d..0358a15b 100644
--- a/docs/html/_modules/PyWGCNA/wgcna.html
+++ b/docs/html/_modules/PyWGCNA/wgcna.html
@@ -1,18 +1,16 @@
-
+
PyWGCNA.wgcna — PyWGCNA documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -102,7 +100,18 @@
-
+
+
+
+
Source code for PyWGCNA.wgcna
import math
@@ -173,8 +182,10 @@ Source code for PyWGCNA.wgcna
BOLD = "\033[1m"
UNDERLINE = "\033[4m"
-[docs]class WGCNA(GeneExp):
- """
+
+[docs]
+class WGCNA(GeneExp):
+ """
A class used to do weighted gene co-expression network analysis.
:param name: name of the WGCNA we used to visualize data (default: 'WGCNA')
@@ -310,8 +321,10 @@ Source code for PyWGCNA.wgcna
self.figureType = figureType
-[docs] def preprocess(self, show=True):
- """
+
+[docs]
+ def preprocess(self, show=True):
+ """
Preprocessing PyWGCNA object including removing obvious outlier on genes and samples
:param show: indicate if you want to show your plot or not (if you put this to False it will not either show and save the plot)
@@ -330,14 +343,14 @@ Source code for PyWGCNA.wgcna
# Optionally, print the gene and sample names that were removed:
if np.size(goodGenes) - np.count_nonzero(goodGenes) > 0:
print(
- f"{OKGREEN} {np.size(goodGenes) - np.count_nonzero(goodGenes)} gene(s) detected as an outlier!{ENDC}")
+ f"{OKGREEN} {np.size(goodGenes) - np.count_nonzero(goodGenes)} gene(s) detected as an outlier!{ENDC}")
print(
- f"{OKGREEN}Removing genes: {', '.join(self.datExpr.var.index[[not goodGene for goodGene in goodGenes]].tolist())}{ENDC}")
+ f"{OKGREEN}Removing genes: {', '.join(self.datExpr.var.index[[not goodGene for goodGene in goodGenes]].tolist())}{ENDC}")
if np.size(goodSamples) - np.count_nonzero(goodSamples) > 0:
print(
- f"{OKGREEN} {np.size(goodSamples) - np.count_nonzero(goodSamples)} sample(s) detected as an outlier!{ENDC}")
+ f"{OKGREEN} {np.size(goodSamples) - np.count_nonzero(goodSamples)} sample(s) detected as an outlier!{ENDC}")
print(
- f"{OKGREEN}Removing samples: {', '.join(self.datExpr.obs.index[[not goodSample for goodSample in goodSamples]].tolist())}{ENDC}")
+ f"{OKGREEN}Removing samples: {', '.join(self.datExpr.obs.index[[not goodSample for goodSample in goodSamples]].tolist())}{ENDC}")
# Remove the offending genes and samples from the data:
self.datExpr = self.datExpr[goodSamples, goodGenes]
@@ -366,8 +379,11 @@ Source code for PyWGCNA.wgcna
print("\tDone pre-processing..\n")
-[docs] def findModules(self, kwargs_function={'cutreeHybrid': {'deepSplit': 2, 'pamRespectsDendro': False}}):
- """
+
+
+[docs]
+ def findModules(self, kwargs_function={'cutreeHybrid': {'deepSplit': 2, 'pamRespectsDendro': False}}):
+ """
Clustering genes through original WGCNA pipeline: 1.pick soft threshold 2.calculating adjacency matrix 3.calculating TOM similarity matrix 4.cluster genes base of dissTOM 5.merge similar cluster dynamically
:param kwargs_function: dictionary where the keys are the name of the function and values are the dictionary contains parameter you want to change within function
@@ -502,8 +518,11 @@ Source code for PyWGCNA.wgcna
print("\tDone running WGCNA..\n")
-[docs] def runWGCNA(self):
- """
+
+
+[docs]
+ def runWGCNA(self):
+ """
Preprocess and find modules
"""
WGCNA.preprocess(self)
@@ -512,8 +531,11 @@ Source code for PyWGCNA.wgcna
return self
-[docs] def analyseWGCNA(self, order=None, geneList=None, show=True, alternative='two-sided'):
- """
+
+
+[docs]
+ def analyseWGCNA(self, order=None, geneList=None, show=True, alternative='two-sided'):
+ """
Analysing results: 1.calculating module trait relationship 2.plotting module heatmap eigengene 3.finding GO term for each module
:param order: indicate in which order metadata will show up in plots (should same as metadata name in anndata)
@@ -580,9 +602,12 @@ Source code for PyWGCNA.wgcna
moduleName=module)
print("\tDone..\n")
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def replaceMissing(x, replaceWith):
- """
+ """
Replacing missing (NA) value with appropriate value (for integer number replace with 0 and for string replace with "")
:param x: value want to replace (single item)
@@ -603,9 +628,12 @@ Source code for PyWGCNA.wgcna
x = x.fillna(replaceWith)
return x
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def checkAndScaleWeights(weights, expr, scaleByMax=True):
- """
+ """
check and scale weights of gene expression
:param weights: weights of gene expression
:type weights: pandas dataframe
@@ -638,11 +666,14 @@ Source code for PyWGCNA.wgcna
return weights
+
# Check that all genes and samples have sufficiently low numbers of missing values.
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def goodSamplesGenes(datExpr, weights=None, minFraction=1 / 2, minNSamples=4, minNGenes=4, tol=None,
minRelativeWeight=0.1):
- """
+ """
Checks data for missing entries, entries with weights below a threshold, and zero-variance genes. If necessary, the filtering is iterated.
:param datExpr:expression data. A data frame in which columns are samples and rows are gene.
@@ -688,11 +719,14 @@ Source code for PyWGCNA.wgcna
return goodGenes, goodSamples, allOK
+
# Filter genes with too many missing entries
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def goodGenesFun(datExpr, weights=None, useSamples=None, useGenes=None, minFraction=1 / 2,
minNSamples=4, minNGenes=4, tol=None, minRelativeWeight=0.1):
- """
+ """
Check data for missing entries and returns a list of genes that have non-zero variance
:param datExpr:expression data. A data frame in which columns are genes and rows ar samples.
@@ -776,11 +810,14 @@ Source code for PyWGCNA.wgcna
return gg
+
# Filter samples with too many missing entries
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def goodSamplesFun(datExpr, weights=None, useSamples=None, useGenes=None, minFraction=1 / 2,
minNSamples=4, minNGenes=4, minRelativeWeight=0.1):
- """
+ """
Check data for missing entries and returns a list of samples that have non-zero variance
:param datExpr:expression data. A data frame in which columns are genes and rows ar samples.
@@ -839,9 +876,12 @@ Source code for PyWGCNA.wgcna
return goodSamples
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def hclust(d, method="complete"):
- """
+ """
Hierarchical cluster analysis on a set of dissimilarities and methods for analyzing it.
:param d: a dissimilarity structure as produced by 'pdist'.
@@ -864,10 +904,13 @@ Source code for PyWGCNA.wgcna
return dendrogram
+
# Determine cluster under the line
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def cutree(sampleTree, cutHeight=50000.0):
- """
+ """
Given a linkage matrix Z, return the cut tree. remove samples/genes/modules base on hierarchical clustering
:param sampleTree: The linkage matrix.
@@ -882,13 +925,16 @@ Source code for PyWGCNA.wgcna
return cutTree
+
# Call the network topology analysis function
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def pickSoftThreshold(data, dataIsExpr=True, weights=None, RsquaredCut=0.9, MeanCut=100, powerVector=None,
nBreaks=10,
blockSize=None, corOptions=None, networkType="unsigned", moreNetworkConcepts=False,
gcInterval=None):
- """
+ """
Analysis of scale free topology for multiple soft thresholding powers.
:param data: expression data in a matrix or data frame. Rows correspond to samples and columns to genes.
@@ -1054,9 +1100,12 @@ Source code for PyWGCNA.wgcna
return powerEstimate, datout
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def checkSimilarity(adjMat, min=-1, max=1):
- """
+ """
check similarity matrix format is correct
:param adjMat: data we want to be checked
@@ -1084,9 +1133,12 @@ Source code for PyWGCNA.wgcna
if all(np.min(adjMat) < min) or all(np.max(adjMat) > max):
sys.exit(("some entries are not between", min, "and", max))
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def calBlockSize(matrixSize, rectangularBlocks=True, maxMemoryAllocation=None, overheadFactor=3):
- """
+ """
find suitable block size for calculating soft power threshold
"""
if maxMemoryAllocation is None:
@@ -1103,10 +1155,13 @@ Source code for PyWGCNA.wgcna
return min(matrixSize, blockSz)
+
# Calculation of fitting statistics for evaluating scale free topology fit.
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def scaleFreeFitIndex(k, nBreaks=10):
- """
+ """
calculates several indices (fitting statistics) for evaluating scale free topology fit.
:param k: numeric list whose components contain non-negative values
@@ -1143,10 +1198,13 @@ Source code for PyWGCNA.wgcna
'truncatedExponentialAdjRsquared': [model2.rsquared_adj]})
return dfout
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def adjacency(datExpr, selectCols=None, adjacencyType="unsigned", power=6, corOptions=pd.DataFrame(), weights=None,
weightArgNames=None):
- """
+ """
Calculates (correlation or distance) network adjacency from given expression data or from a similarity
:param datExpr: data frame containing expression data. Columns correspond to genes and rows to samples.
@@ -1210,9 +1268,12 @@ Source code for PyWGCNA.wgcna
return cor_mat ** power
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def checkAdjMat(adjMat, min=0, max=1):
- """
+ """
check adjacency matrix format is correct
:param adjMat: data we want to be checked
@@ -1237,6 +1298,7 @@ Source code for PyWGCNA.wgcna
if np.min(adjMat) < min or np.max(adjMat) > max:
sys.exit(("some entries are not between", min, "and", max))
+
@staticmethod
def TomSimilarityFromAdj(adjMat, TOMDenom, TOMType):
# Prepare adjacency
@@ -1256,9 +1318,11 @@ Source code for PyWGCNA.wgcna
np.fill_diagonal(tom, 1)
return tom
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def TOMsimilarity(adjMat, TOMType="signed", TOMDenom="min"):
- """
+ """
Calculation of the topological overlap matrix, and the corresponding dissimilarity, from a given adjacency matrix
:param adjMat: adjacency matrix, that is a square, symmetric matrix with entries between 0 and 1 (negative values are allowed if TOMType=="signed").
@@ -1292,6 +1356,7 @@ Source code for PyWGCNA.wgcna
return pd.DataFrame(tom)
+
@staticmethod
def interpolate(data, index):
i = round(index)
@@ -1336,7 +1401,9 @@ Source code for PyWGCNA.wgcna
return merges
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def cutreeHybrid(dendro, distM, cutHeight=None, minClusterSize=20, deepSplit=1,
maxCoreScatter=None, minGap=None, maxAbsCoreScatter=None,
minAbsGap=None, minSplitHeight=None, minAbsSplitHeight=None,
@@ -1345,7 +1412,7 @@ Source code for PyWGCNA.wgcna
assumeSimpleExternalSpecification=True, pamStage=True,
pamRespectsDendro=True, useMedoids=False, maxPamDist=None,
respectSmallClusters=True):
- """
+ """
Detect clusters in a dendorgram produced by the function hclust.
:param dendro: a hierarchical clustering dendorgram such as one returned by hclust.
@@ -1961,9 +2028,12 @@ Source code for PyWGCNA.wgcna
OrdNumLabs.Value = OrdNumLabs.Value - UnlabeledExist
return OrdNumLabs
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def labels2colors(labels, zeroIsGrey=True, colorSeq=None, naColor="grey"):
- """
+ """
Converts a vector or array of numerical labels into a corresponding vector or array of colors corresponding to the labels.
:param labels: list or matrix of non-negative integer or other (such as character) labels.
@@ -2021,10 +2091,13 @@ Source code for PyWGCNA.wgcna
return colors
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def moduleEigengenes(expr, colors, impute=True, nPC=1, align="along average", excludeGrey=False, grey="grey",
subHubs=True, softPower=6, scaleVar=True, trapErrors=False):
- """
+ """
Calculates module eigengenes (1st principal component) of modules in a given single dataset.
:param expr: Expression data for a single set in the form of a data frame where rows are samples and columns are genes (probes).
@@ -2221,6 +2294,7 @@ Source code for PyWGCNA.wgcna
"validMEs": validMEs, "validColors": validColors, "allOK": allOK, "allPC": allPC, "isPC": isPC,
"isHub": isHub, "validAEs": validAEs, "allAEOK": allAEOK}
+
@staticmethod
def permissiveDim(x):
d = x.shape
@@ -2228,9 +2302,11 @@ Source code for PyWGCNA.wgcna
return [len(x), 1]
return d
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def checkSets(data, checkStructure=False, useSets=None):
- """
+ """
Checks whether given sets have the correct format and retrieves dimensions.
:param data: A dict of lists; in each list there must be a component named data whose content is a matrix or dataframe or array of dimension 2.
@@ -2282,9 +2358,12 @@ Source code for PyWGCNA.wgcna
nSamples[set] = WGCNA.permissiveDim(data[set])[0]
return {"nSets": nSets, "nGenes": nGenes, "nSamples": nSamples, "structureOK": structureOK}
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def fixDataStructure(data):
- """
+ """
Encapsulates single-set data in a wrapper that makes the data suitable for functions working on multiset data collections.
:param data: A dataframe, matrix or array with two dimensions to be encapsulated.
@@ -2299,11 +2378,14 @@ Source code for PyWGCNA.wgcna
data = {0: {'data': x}}
return data
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def multiSetMEs(exprData, colors, universalColors=None, useSets=None, useGenes=None, impute=True, nPC=1,
align="along average", excludeGrey=False, subHubs=True, trapErrors=False, softPower=6,
grey=None):
- """
+ """
Calculates module eigengenes for several sets.
:param exprData: Expression data in a multi-set format
@@ -2417,9 +2499,12 @@ Source code for PyWGCNA.wgcna
# names(MEs) = names(exprData)
return MEs
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def consensusMEDissimilarityMajor(MEs, useAbs=False, useSets=None, method="consensus"):
- """
+ """
Calculates consensus dissimilarity (1-cor) of given module eigengenes realized in several sets.
"""
methods = ["consensus", "majority"]
@@ -2454,6 +2539,7 @@ Source code for PyWGCNA.wgcna
return ConsDiss
+
@staticmethod
def clustOrder(distM, greyLast=True, greyName="MEgrey"):
distNames = distM.index
@@ -2487,9 +2573,11 @@ Source code for PyWGCNA.wgcna
order = 1
return order
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def orderMEs(MEs, greyLast=True, greyName="MEgrey", orderBy=0, order=None, useSets=None):
- """
+ """
Reorder given (eigen-)vectors such that similar ones (as measured by correlation) are next to each other.
:param MEs: Module eigengenes in a multi-set format.
@@ -2563,9 +2651,12 @@ Source code for PyWGCNA.wgcna
else:
return orderedMEs[0]['data']
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def consensusOrderMEs(MEs, useAbs=False, useSets=None, greyLast=True, greyName="MEgrey", method="consensus"):
- """
+ """
Reorder given (eigen-)vectors such that similar ones (as measured by correlation) are next to each other.
:param MEs: Module eigengenes of several sets in a multi-set format
@@ -2589,6 +2680,7 @@ Source code for PyWGCNA.wgcna
MEs = WGCNA.orderMEs(MEs, greyLast=greyLast, greyName=greyName, order=order, useSets=useSets)
return MEs
+
@staticmethod
def equalizeQuantilesFun(data, summaryType=["median", "mean"]):
# summaryType = match.arg(summaryType)
@@ -2646,12 +2738,14 @@ Source code for PyWGCNA.wgcna
Branches[np.where(np.logical_not(TrueBranch.iloc[Branches]))[0].tolist()] = 0
return Branches
-[docs] @staticmethod
+
+[docs]
+ @staticmethod
def mergeCloseModules(exprData, colors, MEs=None, useSets=None, impute=True, checkDataFormat=True,
unassdColor="grey", useAbs=False, equalizeQuantiles=False, quantileSummary="mean",
consensusQuantile=0, cutHeight=0.2, iterate=True, relabel=False, colorSeq=None,
getNewMEs=True, getNewUnassdME=True, trapErrors=False):
- """
+ """
Merges modules in gene expression networks that are too close as measured by the correlation of their eigengenes.
:param exprData: Expression data, either a single data frame with rows corresponding to samples and columns to genes, or in a multi-set format.
@@ -2850,8 +2944,11 @@ Source code for PyWGCNA.wgcna
return {"colors": MergedNewColors, "dendro": Tree, "oldDendro": oldTree, "cutHeight": cutHeight,
"oldMEs": oldMEs['data'], "newMEs": newMEs['data'], "allOK": True}
-[docs] def saveWGCNA(self):
- """
+
+
+[docs]
+ def saveWGCNA(self):
+ """
Saves the current WGCNA in pickle format with the .p extension
"""
print(f"{BOLD}{OKBLUE}Saving WGCNA as {self.name}.p{ENDC}")
@@ -2860,8 +2957,11 @@ Source code for PyWGCNA.wgcna
pickle.dump(self, picklefile)
picklefile.close()
-[docs] def getDatTraits(self, metaData):
- """
+
+
+[docs]
+ def getDatTraits(self, metaData):
+ """
get data trait module base on samples information
:return: a dataframe contains information in suitable format for plotting module trait relationship heatmap
@@ -2892,13 +2992,16 @@ Source code for PyWGCNA.wgcna
return datTraits
-[docs] def module_trait_relationships_heatmap(self,
+
+
+[docs]
+ def module_trait_relationships_heatmap(self,
metaData,
alternative='two-sided',
figsize=None,
show=True,
file_name='module-traitRelationships'):
- """
+ """
plot topic-trait relationship heatmap
:param metaData: traits you would like to see the relationship with topics (must be column name of datExpr.obs)
@@ -2965,8 +3068,11 @@ Source code for PyWGCNA.wgcna
if self.save:
fig.savefig(f"{self.outputPath}figures/{file_name}.{self.figureType}")
-[docs] def getModuleName(self):
- """
+
+
+[docs]
+ def getModuleName(self):
+ """
get names of modules
:return: name of modules
@@ -2974,8 +3080,11 @@ Source code for PyWGCNA.wgcna
"""
return np.unique(self.datExpr.var['moduleColors']).tolist()
-[docs] def getGeneModule(self, moduleName):
- """
+
+
+[docs]
+ def getGeneModule(self, moduleName):
+ """
get list of genes corresponding to modules
:param moduleName: name of modules
@@ -2994,8 +3103,11 @@ Source code for PyWGCNA.wgcna
output[color] = self.datExpr.var[self.datExpr.var['moduleColors'] == color]
return output
-[docs] def getModulesGene(self, geneIds):
- """
+
+
+[docs]
+ def getModulesGene(self, geneIds):
+ """
get list of modules corresponding to gene(s)
:param geneIds: gene id
@@ -3016,8 +3128,11 @@ Source code for PyWGCNA.wgcna
return modules
-[docs] def setMetadataColor(self, col, cmap):
- """
+
+
+[docs]
+ def setMetadataColor(self, col, cmap):
+ """
set color pallete for each group of metadata
:param col: name of metadata
@@ -3031,8 +3146,11 @@ Source code for PyWGCNA.wgcna
return None
self.metadataColors[col] = cmap
-[docs] def plotModuleEigenGene(self, moduleName, metadata, show=True):
- """
+
+
+[docs]
+ def plotModuleEigenGene(self, moduleName, metadata, show=True):
+ """
plot module eigen gene figure in given module
:param moduleName: module name
@@ -3046,7 +3164,10 @@ Source code for PyWGCNA.wgcna
height_ratios = []
for m in metadata:
- height_ratios.append(len(list(self.metadataColors[m].keys())))
+ if isinstance(self.metadataColors[m], dict):
+ height_ratios.append(len(list(self.metadataColors[m].keys())))
+ else:
+ height_ratios.append(1)
height_ratios.reverse()
modules = np.unique(self.datExpr.var['moduleColors']).tolist()
@@ -3081,7 +3202,8 @@ Source code for PyWGCNA.wgcna
ax.remove()
ax_legend = fig.add_subplot(gs[:, 1])
ax_legend.axis('off')
- axs_legend = gridspec.GridSpecFromSubplotSpec(len(metadata), 1, subplot_spec=ax_legend,
+ axs_legend = gridspec.GridSpecFromSubplotSpec(len(metadata), 1,
+ subplot_spec=ax_legend.get_subplotspec(),
height_ratios=height_ratios)
for m in metadata:
@@ -3089,15 +3211,28 @@ Source code for PyWGCNA.wgcna
x = ind
y = np.repeat(3000 * metadata.index(m), len(ind))
color = sampleInfo[m].values
- for n in list(self.metadataColors[m].keys()):
- color = np.where(color == n, self.metadataColors[m][n], color)
- patch = mpatches.Patch(color=self.metadataColors[m][n], label=n)
- handles.append(patch)
- axs[0, 0].scatter(x, y, c=color, s=1600, marker='s')
- ax_legend = plt.Subplot(fig, axs_legend[len(metadata) - 1 - metadata.index(m)])
- ax_legend.legend(title=m, handles=handles)
- ax_legend.axis('off')
- fig.add_subplot(ax_legend)
+ if type(self.metadataColors[m]) == dict:
+ for n in list(self.metadataColors[m].keys()):
+ color = np.where(color == n, self.metadataColors[m][n], color)
+ patch = mpatches.Patch(color=self.metadataColors[m][n], label=n)
+ handles.append(patch)
+ axs[0, 0].scatter(x, y, c=color, s=1600, marker='s')
+ ax_legend = plt.Subplot(fig, axs_legend[len(metadata) - 1 - metadata.index(m)])
+ ax_legend.legend(title=m, handles=handles)
+ ax_legend.axis('off')
+ fig.add_subplot(ax_legend)
+ else:
+ axs[0, 0].scatter(x, y, c=color, cmap=self.metadataColors[m].get_cmap(),
+ s=1600, marker='s')
+
+ ax_legend = plt.Subplot(fig, axs_legend[len(metadata) - 1 - metadata.index(m)])
+ clb = fig.colorbar(mappable=self.metadataColors[m],
+ ax=ax_legend,
+ orientation='horizontal',
+ fraction=0.9)
+ clb.ax.set_title(m.capitalize())
+ ax_legend.axis('off')
+ fig.add_subplot(ax_legend)
axs[0, 0].set_title(f"Module Eigengene for {moduleName}", size=28, fontweight="bold")
axs[0, 0].set_ylim(-2000, np.max(y) + 2000)
@@ -3137,8 +3272,11 @@ Source code for PyWGCNA.wgcna
return None
-[docs] def barplotModuleEigenGene(self, moduleName, metadata, combine=True, colorBar=None, show=True):
- """
+
+
+[docs]
+ def barplotModuleEigenGene(self, moduleName, metadata, combine=True, colorBar=None, show=True):
+ """
bar plot of module eigen gene figure in given module
:param moduleName: module name
@@ -3292,8 +3430,11 @@ Source code for PyWGCNA.wgcna
else:
return axs
-[docs] def functional_enrichment_analysis(self, type, moduleName, sets=None, p_value=1, file_name=None, **kwargs):
- """
+
+
+[docs]
+ def functional_enrichment_analysis(self, type, moduleName, sets=None, p_value=1, file_name=None, **kwargs):
+ """
Doing functional enrichment analysis including GO, KEGG and REACTOME
:param type: indicate the type of databases which it should be one of "GO", "KEGG", "REACTOME"
@@ -3364,14 +3505,17 @@ Source code for PyWGCNA.wgcna
p_value=str(p_value))
print(
- f"{numGeneModule - token_result['identifiersNotFound']} out of {numGeneModule} genes (identifiers) in the sample were found in Reactome.")
+ f"{numGeneModule - token_result['identifiersNotFound']} out of {numGeneModule} genes (identifiers) in the sample were found in Reactome.")
print(
f"{token_result['resourceSummary'][0]['pathways']} pathways were hit by at least one of them, which {len(token_result['pathways'])} of them have p-value less than {p_value}.")
print(f"Report was saved {self.outputPath}figures/{type}/{file_name}.{self.figureType}!")
print(f"For more information please visit https://reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS={token}")
-[docs] def updateGeneInfo(self, geneInfo=None, path=None, sep=','):
- """
+
+
+[docs]
+ def updateGeneInfo(self, geneInfo=None, path=None, sep=','):
+ """
add/update genes info in datExpr and geneExpr anndata
:param geneInfo: gene information table you want to add to your data
@@ -3385,8 +3529,11 @@ Source code for PyWGCNA.wgcna
self.geneExpr = GeneExp.updateGeneInfo(self.geneExpr, geneInfo, path, sep)
self.datExpr = GeneExp.updateGeneInfo(self.datExpr, geneInfo, path, sep)
-[docs] def updateSampleInfo(self, sampleInfo=None, path=None, sep=','):
- """
+
+
+[docs]
+ def updateSampleInfo(self, sampleInfo=None, path=None, sep=','):
+ """
add/update metadata in datExpr and geneExpr anndata
:param sampleInfo: Sample information table you want to add to your data
@@ -3400,10 +3547,13 @@ Source code for PyWGCNA.wgcna
self.geneExpr = GeneExp.updateSampleInfo(self.geneExpr, sampleInfo, path, sep)
self.datExpr = GeneExp.updateSampleInfo(self.datExpr, sampleInfo, path, sep)
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def softConnectivity(datExpr, corOptions=pd.DataFrame(), weights=None, type="unsigned", power=6, blockSize=1500,
minNSamples=None):
- """
+ """
Given expression data or a similarity, the function constructs the adjacency matrix and for each node calculates its connectivity, that is the sum of the adjacency to the other nodes.
:param datExpr: a data frame containing the expression data, with rows corresponding to samples and columns to genes.
@@ -3461,9 +3611,12 @@ Source code for PyWGCNA.wgcna
start = end + 1
return k
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def intramodularConnectivity(mat, colors, scaleByMax=False, index=None):
- """
+ """
Calculates intramodular connectivity, i.e., connectivity of nodes to other nodes within the same module.
:param mat: adjacency which should be a square, symmetric matrix with entries between 0 and 1.
@@ -3511,8 +3664,11 @@ Source code for PyWGCNA.wgcna
res.index = index
return res
-[docs] def CalculateSignedKME(self, exprWeights=None, MEWeights=None):
- """
+
+
+[docs]
+ def CalculateSignedKME(self, exprWeights=None, MEWeights=None):
+ """
Calculation of (signed) eigengene-based connectivity, also known as module membership.
:param exprWeights: optional weight matrix of observation weights for datExpr, of the same dimensions as datExpr
@@ -3551,8 +3707,11 @@ Source code for PyWGCNA.wgcna
self.signedKME = pd.DataFrame(output[0:datExpr.shape[1], datExpr.shape[1]:],
index=datExpr.columns, columns=col)
-[docs] def CoexpressionModulePlot(self, modules, numGenes=10, numConnections=100, minTOM=0, filters=None, file_name=None):
- """
+
+
+[docs]
+ def CoexpressionModulePlot(self, modules, numGenes=10, numConnections=100, minTOM=0, filters=None, file_name=None):
+ """
plot Coexpression for given module
:param modules: name of modules you like to plot
@@ -3630,8 +3789,11 @@ Source code for PyWGCNA.wgcna
net.show(f"{self.outputPath}figures/network/{file_name}.html")
-[docs] def PPI_network(self, species, moduleName=None, geneList=None, output_format="image"):
- """
+
+
+[docs]
+ def PPI_network(self, species, moduleName=None, geneList=None, output_format="image"):
+ """
retrieve an image of a STRING network of a neighborhood surrounding one or more proteins or ask STRING to show only the network of interactions between your input proteins.
:param species: NCBI taxon identifiers (e.g. Human is 9606, see: https://string-db.org/cgi/input.pl?input_page_active_form=organisms).
@@ -3683,10 +3845,13 @@ Source code for PyWGCNA.wgcna
request_url=request_url)
return res
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def request_PPI_subset(params,
request_url='https://version-11-5.string-db.org/api/tsv-no-header/interaction_partners'):
- """
+ """
request STRING to find genes interact with our gene list base
:param request_url: suitable url for using STRING API
@@ -3711,10 +3876,13 @@ Source code for PyWGCNA.wgcna
return res
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def request_PPI(genes,
species):
- """
+ """
Getting all the STRING interaction partners of the protein set
:param genes: list of genes you want to find interaction for
@@ -3755,12 +3923,15 @@ Source code for PyWGCNA.wgcna
print(f"{len(res.gene1.unique().tolist())} genes out of {len(genes)} genes have PPI.")
return res
-[docs] @staticmethod
+
+
+[docs]
+ @staticmethod
def request_PPI_image(params,
genes,
file_name,
request_url='https://version-11-5.string-db.org/api/image/network'):
- """
+ """
plot PPI interaction along with link that direct you to the STRING webpage
:param params: parameters for requesting
@@ -3787,8 +3958,11 @@ Source code for PyWGCNA.wgcna
sleep(1)
-[docs] def top_n_hub_genes(self, moduleName, n=10):
- """
+
+
+[docs]
+ def top_n_hub_genes(self, moduleName, n=10):
+ """
find top n hub genes based on connectivity in given module
:param moduleName: name of module you want to top n hub genes
@@ -3818,7 +3992,9 @@ Source code for PyWGCNA.wgcna
hub_genes = pd.concat([hub_genes, datExpr.var], axis=1)
hub_genes = hub_genes.iloc[:n, :]
- return hub_genes
+ return hub_genes
+
+
@@ -3833,7 +4009,7 @@ Source code for PyWGCNA.wgcna
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
index 6c01a43d..10f5debe 100644
--- a/docs/html/_modules/index.html
+++ b/docs/html/_modules/index.html
@@ -1,18 +1,16 @@
-
+
Overview: module code — PyWGCNA documentation
-
-
-
-
-
-
-
-
+
+
+
+
+
+
@@ -102,7 +100,18 @@
-
+
+
+
+
All modules for which code is available
- PyWGCNA.comparison
@@ -123,7 +132,7 @@ All modules for which code is available
© Copyright 2022, Narges Rezaie.
- Created using Sphinx 5.0.2.
+ Created using Sphinx 7.4.7.
diff --git a/docs/html/_static/_sphinx_javascript_frameworks_compat.js b/docs/html/_static/_sphinx_javascript_frameworks_compat.js
deleted file mode 100644
index 8549469d..00000000
--- a/docs/html/_static/_sphinx_javascript_frameworks_compat.js
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- * _sphinx_javascript_frameworks_compat.js
- * ~~~~~~~~~~
- *
- * Compatability shim for jQuery and underscores.js.
- *
- * WILL BE REMOVED IN Sphinx 6.0
- * xref RemovedInSphinx60Warning
- *
- */
-
-/**
- * select a different prefix for underscore
- */
-$u = _.noConflict();
-
-
-/**
- * small helper function to urldecode strings
- *
- * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
- */
-jQuery.urldecode = function(x) {
- if (!x) {
- return x
- }
- return decodeURIComponent(x.replace(/\+/g, ' '));
-};
-
-/**
- * small helper function to urlencode strings
- */
-jQuery.urlencode = encodeURIComponent;
-
-/**
- * This function returns the parsed url parameters of the
- * current request. Multiple values per key are supported,
- * it will always return arrays of strings for the value parts.
- */
-jQuery.getQueryParameters = function(s) {
- if (typeof s === 'undefined')
- s = document.location.search;
- var parts = s.substr(s.indexOf('?') + 1).split('&');
- var result = {};
- for (var i = 0; i < parts.length; i++) {
- var tmp = parts[i].split('=', 2);
- var key = jQuery.urldecode(tmp[0]);
- var value = jQuery.urldecode(tmp[1]);
- if (key in result)
- result[key].push(value);
- else
- result[key] = [value];
- }
- return result;
-};
-
-/**
- * highlight a given string on a jquery object by wrapping it in
- * span elements with the given class name.
- */
-jQuery.fn.highlightText = function(text, className) {
- function highlight(node, addItems) {
- if (node.nodeType === 3) {
- var val = node.nodeValue;
- var pos = val.toLowerCase().indexOf(text);
- if (pos >= 0 &&
- !jQuery(node.parentNode).hasClass(className) &&
- !jQuery(node.parentNode).hasClass("nohighlight")) {
- var span;
- var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
- if (isInSVG) {
- span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
- } else {
- span = document.createElement("span");
- span.className = className;
- }
- span.appendChild(document.createTextNode(val.substr(pos, text.length)));
- node.parentNode.insertBefore(span, node.parentNode.insertBefore(
- document.createTextNode(val.substr(pos + text.length)),
- node.nextSibling));
- node.nodeValue = val.substr(0, pos);
- if (isInSVG) {
- var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
- var bbox = node.parentElement.getBBox();
- rect.x.baseVal.value = bbox.x;
- rect.y.baseVal.value = bbox.y;
- rect.width.baseVal.value = bbox.width;
- rect.height.baseVal.value = bbox.height;
- rect.setAttribute('class', className);
- addItems.push({
- "parent": node.parentNode,
- "target": rect});
- }
- }
- }
- else if (!jQuery(node).is("button, select, textarea")) {
- jQuery.each(node.childNodes, function() {
- highlight(this, addItems);
- });
- }
- }
- var addItems = [];
- var result = this.each(function() {
- highlight(this, addItems);
- });
- for (var i = 0; i < addItems.length; ++i) {
- jQuery(addItems[i].parent).before(addItems[i].target);
- }
- return result;
-};
-
-/*
- * backward compatibility for jQuery.browser
- * This will be supported until firefox bug is fixed.
- */
-if (!jQuery.browser) {
- jQuery.uaMatch = function(ua) {
- ua = ua.toLowerCase();
-
- var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
- /(webkit)[ \/]([\w.]+)/.exec(ua) ||
- /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
- /(msie) ([\w.]+)/.exec(ua) ||
- ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
- [];
-
- return {
- browser: match[ 1 ] || "",
- version: match[ 2 ] || "0"
- };
- };
- jQuery.browser = {};
- jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
-}
diff --git a/docs/html/_static/basic.css b/docs/html/_static/basic.css
index 7d5974c3..f316efcb 100644
--- a/docs/html/_static/basic.css
+++ b/docs/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -236,17 +236,11 @@ div.body p, div.body dd, div.body li, div.body blockquote {
a.headerlink {
visibility: hidden;
}
-a.brackets:before,
-span.brackets > a:before{
- content: "[";
-}
-a.brackets:after,
-span.brackets > a:after {
- content: "]";
+a:visited {
+ color: #551A8B;
}
-
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
@@ -334,11 +328,17 @@ aside.sidebar {
p.sidebar-title {
font-weight: bold;
}
+
+nav.contents,
+aside.topic,
div.admonition, div.topic, blockquote {
clear: left;
}
/* -- topics ---------------------------------------------------------------- */
+
+nav.contents,
+aside.topic,
div.topic {
border: 1px solid #ccc;
padding: 7px;
@@ -377,6 +377,8 @@ div.body p.centered {
div.sidebar > :last-child,
aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
div.topic > :last-child,
div.admonition > :last-child {
margin-bottom: 0;
@@ -384,6 +386,8 @@ div.admonition > :last-child {
div.sidebar::after,
aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
div.topic::after,
div.admonition::after,
blockquote::after {
@@ -609,25 +613,6 @@ ul.simple p {
margin-bottom: 0;
}
-/* Docutils 0.17 and older (footnotes & citations) */
-dl.footnote > dt,
-dl.citation > dt {
- float: left;
- margin-right: 0.5em;
-}
-
-dl.footnote > dd,
-dl.citation > dd {
- margin-bottom: 0em;
-}
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
- content: "";
- clear: both;
-}
-
-/* Docutils 0.18+ (footnotes & citations) */
aside.footnote > span,
div.citation > span {
float: left;
@@ -652,8 +637,6 @@ div.citation > p:last-of-type:after {
clear: both;
}
-/* Footnotes & citations ends */
-
dl.field-list {
display: grid;
grid-template-columns: fit-content(30%) auto;
@@ -666,10 +649,6 @@ dl.field-list > dt {
padding-right: 5px;
}
-dl.field-list > dt:after {
- content: ":";
-}
-
dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
@@ -695,6 +674,16 @@ dd {
margin-left: 30px;
}
+.sig dd {
+ margin-top: 0px;
+ margin-bottom: 0px;
+}
+
+.sig dl {
+ margin-top: 0px;
+ margin-bottom: 0px;
+}
+
dl > dd:last-child,
dl > dd:last-child > :last-child {
margin-bottom: 0;
@@ -763,6 +752,14 @@ abbr, acronym {
cursor: help;
}
+.translated {
+ background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+ background-color: rgba(255, 207, 207, 0.2)
+}
+
/* -- code displays --------------------------------------------------------- */
pre {
diff --git a/docs/html/_static/doctools.js b/docs/html/_static/doctools.js
index c3db08d1..4d67807d 100644
--- a/docs/html/_static/doctools.js
+++ b/docs/html/_static/doctools.js
@@ -4,12 +4,19 @@
*
* Base JavaScript utilities for all Sphinx HTML documentation.
*
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
"use strict";
+const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([
+ "TEXTAREA",
+ "INPUT",
+ "SELECT",
+ "BUTTON",
+]);
+
const _ready = (callback) => {
if (document.readyState !== "loading") {
callback();
@@ -18,73 +25,11 @@ const _ready = (callback) => {
}
};
-/**
- * highlight a given string on a node by wrapping it in
- * span elements with the given class name.
- */
-const _highlight = (node, addItems, text, className) => {
- if (node.nodeType === Node.TEXT_NODE) {
- const val = node.nodeValue;
- const parent = node.parentNode;
- const pos = val.toLowerCase().indexOf(text);
- if (
- pos >= 0 &&
- !parent.classList.contains(className) &&
- !parent.classList.contains("nohighlight")
- ) {
- let span;
-
- const closestNode = parent.closest("body, svg, foreignObject");
- const isInSVG = closestNode && closestNode.matches("svg");
- if (isInSVG) {
- span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
- } else {
- span = document.createElement("span");
- span.classList.add(className);
- }
-
- span.appendChild(document.createTextNode(val.substr(pos, text.length)));
- parent.insertBefore(
- span,
- parent.insertBefore(
- document.createTextNode(val.substr(pos + text.length)),
- node.nextSibling
- )
- );
- node.nodeValue = val.substr(0, pos);
-
- if (isInSVG) {
- const rect = document.createElementNS(
- "http://www.w3.org/2000/svg",
- "rect"
- );
- const bbox = parent.getBBox();
- rect.x.baseVal.value = bbox.x;
- rect.y.baseVal.value = bbox.y;
- rect.width.baseVal.value = bbox.width;
- rect.height.baseVal.value = bbox.height;
- rect.setAttribute("class", className);
- addItems.push({ parent: parent, target: rect });
- }
- }
- } else if (node.matches && !node.matches("button, select, textarea")) {
- node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
- }
-};
-const _highlightText = (thisNode, text, className) => {
- let addItems = [];
- _highlight(thisNode, addItems, text, className);
- addItems.forEach((obj) =>
- obj.parent.insertAdjacentElement("beforebegin", obj.target)
- );
-};
-
/**
* Small JavaScript module for the documentation.
*/
const Documentation = {
init: () => {
- Documentation.highlightSearchWords();
Documentation.initDomainIndexTable();
Documentation.initOnKeyListeners();
},
@@ -126,51 +71,6 @@ const Documentation = {
Documentation.LOCALE = catalog.locale;
},
- /**
- * highlight the search words provided in the url in the text
- */
- highlightSearchWords: () => {
- const highlight =
- new URLSearchParams(window.location.search).get("highlight") || "";
- const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
- if (terms.length === 0) return; // nothing to do
-
- // There should never be more than one element matching "div.body"
- const divBody = document.querySelectorAll("div.body");
- const body = divBody.length ? divBody[0] : document.querySelector("body");
- window.setTimeout(() => {
- terms.forEach((term) => _highlightText(body, term, "highlighted"));
- }, 10);
-
- const searchBox = document.getElementById("searchbox");
- if (searchBox === null) return;
- searchBox.appendChild(
- document
- .createRange()
- .createContextualFragment(
- '' +
- '' +
- Documentation.gettext("Hide Search Matches") +
- "
"
- )
- );
- },
-
- /**
- * helper function to hide the search marks again
- */
- hideSearchWords: () => {
- document
- .querySelectorAll("#searchbox .highlight-link")
- .forEach((el) => el.remove());
- document
- .querySelectorAll("span.highlighted")
- .forEach((el) => el.classList.remove("highlighted"));
- const url = new URL(window.location);
- url.searchParams.delete("highlight");
- window.history.replaceState({}, "", url);
- },
-
/**
* helper function to focus on search bar
*/
@@ -210,15 +110,11 @@ const Documentation = {
)
return;
- const blacklistedElements = new Set([
- "TEXTAREA",
- "INPUT",
- "SELECT",
- "BUTTON",
- ]);
document.addEventListener("keydown", (event) => {
- if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
- if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
+ // bail for input elements
+ if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return;
+ // bail with special keys
+ if (event.altKey || event.ctrlKey || event.metaKey) return;
if (!event.shiftKey) {
switch (event.key) {
@@ -240,10 +136,6 @@ const Documentation = {
event.preventDefault();
}
break;
- case "Escape":
- if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
- Documentation.hideSearchWords();
- event.preventDefault();
}
}
diff --git a/docs/html/_static/documentation_options.js b/docs/html/_static/documentation_options.js
index a750e4d5..7e4c114f 100644
--- a/docs/html/_static/documentation_options.js
+++ b/docs/html/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
- URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
VERSION: '',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
@@ -10,5 +9,5 @@ var DOCUMENTATION_OPTIONS = {
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false,
SHOW_SEARCH_SUMMARY: true,
- ENABLE_SEARCH_SHORTCUTS: false,
+ ENABLE_SEARCH_SHORTCUTS: true,
};
\ No newline at end of file
diff --git a/docs/html/_static/graphviz.css b/docs/html/_static/graphviz.css
index 19e7afd3..027576e3 100644
--- a/docs/html/_static/graphviz.css
+++ b/docs/html/_static/graphviz.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- graphviz extension.
*
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/html/_static/jquery-3.6.0.js b/docs/html/_static/jquery-3.6.0.js
deleted file mode 100644
index fc6c299b..00000000
--- a/docs/html/_static/jquery-3.6.0.js
+++ /dev/null
@@ -1,10881 +0,0 @@
-/*!
- * jQuery JavaScript Library v3.6.0
- * https://jquery.com/
- *
- * Includes Sizzle.js
- * https://sizzlejs.com/
- *
- * Copyright OpenJS Foundation and other contributors
- * Released under the MIT license
- * https://jquery.org/license
- *
- * Date: 2021-03-02T17:08Z
- */
-( function( global, factory ) {
-
- "use strict";
-
- if ( typeof module === "object" && typeof module.exports === "object" ) {
-
- // For CommonJS and CommonJS-like environments where a proper `window`
- // is present, execute the factory and get jQuery.
- // For environments that do not have a `window` with a `document`
- // (such as Node.js), expose a factory as module.exports.
- // This accentuates the need for the creation of a real `window`.
- // e.g. var jQuery = require("jquery")(window);
- // See ticket #14549 for more info.
- module.exports = global.document ?
- factory( global, true ) :
- function( w ) {
- if ( !w.document ) {
- throw new Error( "jQuery requires a window with a document" );
- }
- return factory( w );
- };
- } else {
- factory( global );
- }
-
-// Pass this if window is not defined yet
-} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-
-// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
-// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
-// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
-// enough that all such attempts are guarded in a try block.
-"use strict";
-
-var arr = [];
-
-var getProto = Object.getPrototypeOf;
-
-var slice = arr.slice;
-
-var flat = arr.flat ? function( array ) {
- return arr.flat.call( array );
-} : function( array ) {
- return arr.concat.apply( [], array );
-};
-
-
-var push = arr.push;
-
-var indexOf = arr.indexOf;
-
-var class2type = {};
-
-var toString = class2type.toString;
-
-var hasOwn = class2type.hasOwnProperty;
-
-var fnToString = hasOwn.toString;
-
-var ObjectFunctionString = fnToString.call( Object );
-
-var support = {};
-
-var isFunction = function isFunction( obj ) {
-
- // Support: Chrome <=57, Firefox <=52
- // In some browsers, typeof returns "function" for HTML