def histProportionTypeNeighbors(distance, dir_out, logFile):
"""Draw proportion type neighbor
in: Distance Max study, log file_data
out: excecute CMD -> draw plot"""
listStruct = structure.ListSub()
listStruct.append("GlobalAmine")
listStruct.append("Global")
for type in listStruct:
file_data = dir_out + "globalProportionType/" + "proportionType" + type + str("%.2f" % distance)
if tool.checkFileEmpty(file_data) == 1:
continue
cmd = (
pathManage.scriptR()
+ "barplotTypeNumberOfneighbors.R "
+ file_data
+ " "
+ type
+ " "
+ str("%.2f" % distance)
)
print cmd
logFile.write(cmd + "\n")
system(cmd)
def barplotCombination(p_filin, logFile, debug=1):
repScript = pathManage.scriptR()
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = repScript + "barplotCombination.R " + p_filin
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def histDistance(p_filin, type_distance):
"""Draw CN length histogram and coplar histogram
in: nameFile data, option for execute R script
out: execute R script -> draw histogram distance"""
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = pathManage.scriptR() + "distance.R " + str(p_filin) + " " + str(type_distance)
print cmd
system(cmd)
def plotDistanceDensity(p_filin, logFile, debug=1):
"""Plot density"""
repScript = pathManage.scriptR()
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = repScript + "densityDistance.R " + p_filin
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def barplotQuantity(distance, type_study, p_filin, logFile, debug=1):
"""Plot count statistic
in: distance for legend plot, type histogram (coplar or length), p_filin with data, type of study, logFile
out: CMD in terminal -> plot """
if tool.checkFileEmpty(p_filin) == 1:
return
rep = pathManage.scriptR()
cmd = rep + "barplotQuantity.R " + p_filin + " " + str("%.2f" % distance) + " " + type_study
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def plotNbNeighbor(p_filin, logFile, debug=1):
"""Plot number neighbor
in: distance for legend plot, type histogram (coplar or length), file with data, type of study, logFile
out: CMD in terminal -> plot """
repScript = pathManage.scriptR()
if tool.checkFileEmpty(p_filin) == 1:
return
cmd = repScript + "plotNumberNeighbor.R " + p_filin
if debug:
print cmd
logFile.write(cmd + "\n")
system(cmd)
def histGlobalProportion(dir_out, logFile):
"""Proportion for each atom
in: log file
out: execute -> CMD
"""
repScript = pathManage.scriptR()
file = dir_out + "GlobalproportionCounterIonGlobal"
if tool.checkFileEmpty(file) == 1:
return
cmd = repScript + "barplotProportionGlobalRef.R " + file
logFile.write(cmd + "\n")
print cmd
system(cmd)
def histProportion(distance, dir_in, logFile):
"""Draw proportion type neighbor
in: Distance Max study, log path_file
out: excecute CMD -> draw plot"""
repScript = pathManage.scriptR()
listType = structure.ListSub()
listType.append("Global")
listType.append("GlobalAmine")
for type in listType:
path_file = dir_in + "globalProportionAtom/" + "proportionAtom" + type + str("%.2f" % distance)
if tool.checkFileEmpty(path_file) == 1:
continue
cmd = repScript + "barplotQuantityGlobalAnalysis.R " + type + " " + path_file + " " + str(distance)
print cmd
system(cmd)
logFile.write(cmd + "\n")
def barplotQuantityByAA(distance, aminoAcid, path_file, logFile):
"""to do"""
if tool.checkFileEmpty(path_file) == 1:
return
rep = pathManage.scriptR()
cmd = (
rep
+ "barplotQuantityByAA.R "
+ path_file
+ " "
+ str("%.2f" % distance)
+ " "
+ aminoAcid
+ " "
+ str("%.2f" % distance)
)
print cmd
logFile.write(cmd + "\n")
system(cmd)
