def plot_mat4seq(filename='default',
data=[],
seq1=[],
seq1lab='Chain 1',
seq1offset=0,
features1=[],
seq2=[],
seq2lab='Chain 2',
seq2offset=0,
features2=[],
title=''):
"""
will plot a 2D matrix for intersection of two sequences
data is a dataframe with three columns Resid1, Resid2, Value.
Resids - 0 based numbering, or offset specified
you have to have zeros for non interacting residue(!)
"""
tempdf = os.path.join(CONFIG.TEMP_DIR, 'temp.csv')
temppng1 = os.path.join(CONFIG.TEMP_DIR, 'tempprofseq1.png')
temppng2 = os.path.join(CONFIG.TEMP_DIR, 'tempprofseq2.png')
lenseq1 = len(seq1[0])
lenseq2 = len(seq2[0])
# print profile
#convert matrix to a dataframe
# df=pd.DataFrame(np.array([profile,range(len(profile))]).T,columns=[axis,'Resid'])
data.to_csv(tempdf, index=False)
shade_aln2png(seq1,
filename=temppng1,
shading_modes=['charge_functional'],
legend=False,
features=features1,
title='',
logo=False,
hideseqs=False,
splitN=20,
setends=[],
ruler=False,
show_seq_names=False,
show_seq_length=False)
shade_aln2png(seq2,
filename=temppng2,
shading_modes=['charge_functional'],
legend=False,
features=features2,
title='',
logo=False,
hideseqs=False,
splitN=20,
setends=[],
ruler=False,
show_seq_names=False,
show_seq_length=False,
rotate=True)
#let's write an R-script
a = open(os.path.join(CONFIG.TEMP_DIR, 'mat4seq.r'), 'w')
a.write(r"""
library(ggplot2)
library(fitdistrplus)
library(gtools)
library(png)
library(grid)
library(reshape2)
library(gridExtra)
library(plyr)""")
a.write("""
df<-read.csv("%s",skip=0,header=TRUE,check.name=FALSE)
img1 <- readPNG("%s")
img2 <- readPNG("%s")
""" % (tempdf, temppng1, temppng2))
a.write("""
seqimg1 <- rasterGrob(img1, interpolate=TRUE,width=1)
seqimg2 <- rasterGrob(img2, interpolate=TRUE,height=1)
theme_set(theme_bw(base_size=24)+theme(panel.border =element_rect(linetype = "dashed", colour = "white")))
a<-ggplot(data=df,aes(x=Resid1+1-%d,y=Resid2+1-%d,color=Value))+
xlab("%s")+
ylab("%s")+
xlim(%f,%f)+
ylim(%f,%f)+
ggtitle("%s")+
# geom_hline(yintercept = c_c$PROT2_resid, colour="green", linetype = "longdash",size=0.5)+
# geom_vline(xintercept = h2azimp, colour="green", linetype = "longdash",size=0.5)+
geom_point(size=5)+scale_colour_gradient(low="blue", high="red",name="Value")+
annotation_custom(seqimg1, ymin=%f, ymax=0, xmin=0.5,xmax=%f)+
annotation_custom(seqimg2, xmin=%f,xmax=0,ymin=0.5, ymax=%f)
"""%(seq1offset,seq2offset,seq1lab,seq2lab,\
-lenseq1*0.05,lenseq1*1.01,-lenseq2*0.05,lenseq2*1.01,\
title[-lenseq1:len(title)],\
-lenseq2*0.05,lenseq1+0.5,\
-lenseq1*0.05,lenseq2+0.5))
a.write("""
ggsave("%s",plot=a,height=%f,width=%f)
""" % (filename if filename[-3:] == 'png' else
(filename + '.png'), 12. / 60. * lenseq2 + 3, 12. / 60. * lenseq1 + 3))
a.close()
os.system('R --vanilla --slave < ' +
os.path.join(CONFIG.TEMP_DIR, 'mat4seq.r'))
os.system('rm Rplots.pdf')
def plot_prof4seq(filename='default',
profile=[],
seqmsa=[],
features=[],
axis='X',
title='',
offset=0.,
funcgroups=None,
seqontop=False,
ruler=False,
htune=1.0,
ltune=1.0,
oy=0.0,
type='bar',
bwidth=0.7,
fontsize=18):
"""
will plot a profile for every position in a sequence or small msa
profile is a list of values.
oy - y lower lim
type='bar' or 'point'
"""
tempdf = os.path.join(CONFIG.TEMP_DIR, 'temp.csv')
temppng = os.path.join(CONFIG.TEMP_DIR, 'tempprofseq.png')
# print profile
#convert profile to a dataframe
if (seqontop):
df = pd.DataFrame(np.array(
[profile, range(len(profile)),
list(str(seqmsa[0].seq))]).T,
columns=['axis', 'Resid', 'seq'])
else:
df = pd.DataFrame(np.array([profile, range(len(profile))]).T,
columns=['axis', 'Resid'])
df.to_csv(tempdf, index=False)
shade_aln2png(seqmsa,
filename=temppng,
shading_modes=['charge_functional'],
legend=False,
features=features,
title='',
logo=False,
hideseqs=False,
splitN=20,
setends=[],
ruler=ruler,
show_seq_names=False,
show_seq_length=False,
funcgroups=funcgroups)
#let's write an R-script
a = open(os.path.join(CONFIG.TEMP_DIR, 'prof4seq.r'), 'w')
a.write(r"""
library(ggplot2)
#library(fitdistrplus)
#library(gtools)
library(png)
library(grid)
#library(reshape2)
#library(gridExtra)
#library(plyr)""")
a.write("""
df<-read.csv("%s",skip=0,header=TRUE,check.name=FALSE)
img <- readPNG("%s")
""" % (tempdf, temppng))
a.write("""
seqimg <- rasterGrob(img, interpolate=TRUE,width=1)
theme_set(theme_bw(base_size=%d)+theme(panel.border =element_rect(linetype = "dashed", colour = "white")))
a<-ggplot(data=df,aes(x=Resid+1+%f,y=axis))+
geom_%s(stat='identity',position='identity',width=%f)+#scale_y_continuous(limits=c(-5,6),breaks=seq(0,6),labels=seq(0,6,by=1))+
%s geom_line(stat='identity',position='identity')+
# scale_x_continuous(limits=c(0,136),labels=c(),breaks=c(),expand=c(0,0))+
# scale_fill_manual(breaks=c('CA','bSCH','amore'),values=c('amore'='red','CA'='blue','bSCH'='green'),labels=c(expression(paste('C',alpha,'-atoms')),'Side chain','> 6Å '),name='')+
# scale_color_manual(breaks=c('CA','bSCH','amore'),values=c('amore'='red','CA'='blue','bSCH'='green'),labels=c(expression(paste('C',alpha,'-atoms')),'Side chain','> 6Å '),name='')+
xlab('Resid')+
ylim(%f,%f)+
# geom_point(data=h3data_amore,aes(color=color),fill='red',size=2)+
ylab("%s")+
ggtitle("%s")+
annotation_custom(seqimg, ymin=%f, ymax=%f, xmin=0.5,xmax=%f)""" %
(fontsize, offset, type, bwidth, ' ' if type == 'point' else '#',
(-max(profile) * 1.01 * ltune + oy), max(profile) * 1.01, axis,
title[-len(profile):len(title)], -max(profile) * ltune + oy, oy,
len(profile) + 0.5))
if (seqontop):
a.write(
"""+geom_text(aes(x=Resid+1+%f-0.25,label=seq),hjust=0, vjust=%f)"""
% (offset, -max(profile) * 0.5))
else:
a.write("""
""")
a.write("""
ggsave("%s",plot=a,height=%f,width=%f)
""" % (filename if filename[-3:] == 'png' else
(filename + '.png'), 4.0 * htune, 12. / 60. * len(profile)))
a.close()
os.system('R --vanilla --slave < %s' %
os.path.join(CONFIG.TEMP_DIR, 'prof4seq.r'))
os.system('rm Rplots.pdf')
def plot_2prof4seq(filename='default',
profile=[],
profile2=[],
seqmsa=[],
features=[],
axis='X',
axis2='X2',
title='',
offset=0.,
funcgroups=None,
ruler=False,
htune=1.0,
ltune=1.0):
"""
thes same as plot_prof4seq but two profiles
profiles should be of the same length!
"""
tempdf = TEMP_DIR + '/temp.csv'
temppng = TEMP_DIR + '/tempprofseq.png'
# print profile
#convert profile to a dataframe
df = pd.DataFrame(np.array([profile, profile2,
range(len(profile))]).T,
columns=[axis, axis2, 'Resid'])
df.to_csv(tempdf, index=False)
shade_aln2png(seqmsa,
filename=temppng,
shading_modes=['charge_functional'],
legend=False,
features=features,
title='',
logo=False,
hideseqs=False,
splitN=20,
setends=[],
ruler=ruler,
show_seq_names=False,
show_seq_length=False,
funcgroups=funcgroups)
#let's write an R-script
a = open(os.path.join(CONFIG.TEMP_DIR, 'prof4seq.r'), 'w')
a.write(r"""
library(ggplot2)
library(fitdistrplus)
library(gtools)
library(png)
library(grid)
library(reshape2)
library(gridExtra)
library(plyr)""")
a.write("""
df<-read.csv("%s",skip=0,header=TRUE,check.name=FALSE)
img <- readPNG("%s")
""" % (tempdf, temppng))
a.write("""
seqimg <- rasterGrob(img, interpolate=TRUE,width=1)
theme_set(theme_bw()+theme(panel.border =element_rect(linetype = "dashed", colour = "white")))
ndf <- melt(df, id="Resid")
a<-ggplot(data=ndf,aes(x=Resid+1+%f,y=value,fill=variable))+
geom_bar(stat='identity',position='dodge')+#scale_y_continuous(limits=c(-5,6),breaks=seq(0,6),labels=seq(0,6,by=1))+
# scale_x_continuous(limits=c(0,136),labels=c(),breaks=c(),expand=c(0,0))+
# scale_fill_manual(breaks=c('CA','bSCH','amore'),values=c('amore'='red','CA'='blue','bSCH'='green'),labels=c(expression(paste('C',alpha,'-atoms')),'Side chain','> 6Å '),name='')+
# scale_color_manual(breaks=c('CA','bSCH','amore'),values=c('amore'='red','CA'='blue','bSCH'='green'),labels=c(expression(paste('C',alpha,'-atoms')),'Side chain','> 6Å '),name='')+
xlab('Resid')+
ylim(%f,%f)+
# geom_point(data=h3data_amore,aes(color=color),fill='red',size=2)+
#ylab("RMSD, Å")+
ggtitle("%s")+
annotation_custom(seqimg, ymin=%f, ymax=0, xmin=0.5,xmax=%f)
""" % (offset, -max(profile) * 1.01 * ltune, max(profile) * 1.01,
title[-len(profile):len(title)], -max(profile) * ltune,
len(profile) + 0.5))
a.write("""
ggsave("%s",plot=a,height=%f,width=%f)
""" % (filename if filename[-3:] == 'png' else
(filename + '.png'), 4.0 * htune, 12. / 60. * len(profile)))
a.close()
os.system('R --vanilla --slave < ' +
os.path.join(CONFIG.TEMP_DIR, 'prof4seq.r'))
def plot_manyprof4seq(filename='default',
profiledf=[[]],
seqmsa=[],
features=[],
axis='X',
title='',
offset=0.,
yoffset=0.,
funcgroups=None,
seqontop=False,
ruler=False,
htune=1.0,
ltune=1.0,
wtune=1.0,
oy=0.0,
type='bar',
bwidth=0.2,
xbreaksby=2,
base_size=24,
psize=1.0,
lsize=1.0,
seqmargin=None,
spacing=1,
dropnan=False,
vline=None,
vlsize=0.0,
xlab=None,
scale_color=None,
scale_x=None,
scale_y=None,
dpi=300):
"""
will plot several profile for every position in a sequence or small msa
profiledf now is a pandas dataframe with columns to be plotted.
oy - y lower lim
type='bar' or 'point'
profiledf - is a dataframe
spacing just divides all indexes (1-based) in array by spacing
"""
tempdf = TEMP_DIR + '/temp.csv'
temppng = TEMP_DIR + '/tempprofseq.png'
# print profile
#convert profile to a dataframe
ldf = len(profiledf)
mdf = max(list(profiledf.max()))
df = pd.concat([
profiledf,
pd.DataFrame(np.arange(1.0,
float(ldf) + 1.0).T / spacing,
columns=['Resid'])
],
axis=1)
df.to_csv(tempdf, index=False)
shade_aln2png(seqmsa,
filename=temppng,
shading_modes=['charge_functional'],
legend=False,
features=features,
title='',
logo=False,
hideseqs=False,
splitN=20,
setends=[],
ruler=ruler,
show_seq_names=False,
show_seq_length=False,
funcgroups=funcgroups,
margins=seqmargin)
if ('expression' not in axis):
axis = '"' + axis + '"'
#let's write an R-script
a = open(os.path.join(CONFIG.TEMP_DIR, 'prof4seq.r', 'w'))
a.write(r"""
library(ggplot2)
library(fitdistrplus)
library(gtools)
library(png)
library(grid)
library(reshape2)
library(gridExtra)
library(plyr)""")
a.write("""
df<-read.csv("%s",skip=0,header=TRUE,check.name=FALSE)
img <- readPNG("%s")
""" % (tempdf, temppng))
a.write("""
seqimg <- rasterGrob(img, interpolate=TRUE,width=1)
theme_set(theme_bw(base_size=%d)+theme(plot.margin=unit(c(0,0,0,0),"mm"),panel.border =element_rect(linetype = "dashed", colour = "white")))
ndf <- melt(df, id="Resid")
if(%s){
ndf=ndf[!is.na(ndf$value),]}
a<-ggplot(data=ndf,aes(x=Resid+%f,y=value+%f,fill=variable,color=variable))+
%s geom_vline(xintercept = %s,size=%f)+
geom_%s(stat='identity'%s)+#scale_y_continuous(limits=c(-5,6),breaks=seq(0,6),labels=seq(0,6,by=1))+
%s geom_line(stat='identity',position='identity',size=%f)+
# scale_x_continuous(limits=c(0,136),labels=c(),breaks=c(),expand=c(0,0))+
# scale_fill_manual(breaks=c('CA','bSCH','amore'),values=c('amore'='red','CA'='blue','bSCH'='green'),labels=c(expression(paste('C',alpha,'-atoms')),'Side chain','> 6Å '),name='')+
# scale_color_manual(breaks=c('CA','bSCH','amore'),values=c('amore'='red','CA'='blue','bSCH'='green'),labels=c(expression(paste('C',alpha,'-atoms')),'Side chain','> 6Å '),name='')+
xlab('%s')+
%s+
ylim(%f,%f)+
%s+
# geom_point(data=h3data_amore,aes(color=color),fill='red',size=2)+
ylab(%s)+
ggtitle("%s")+
scale_x_continuous(limits=c(%d,%d),breaks = seq(%d, %d, by = %d))+
%s+
annotation_custom(seqimg, ymin=%f, ymax=%f, xmin=%f,xmax=%f)"""%(base_size,'TRUE' if dropnan else 'FALSE',\
offset,yoffset, '' if vline!=None else '#', vline if vline!=None else '0.0',vlsize,type,',position=\'dodge\',width=%f'%bwidth if type == 'bar' else ',\
size=%f' %psize,' ' if (type == 'point') or (type=='line') else '#',lsize,\
xlab if xlab else 'Resid',\
scale_color if scale_color else '#',\
(-mdf*1.01*ltune+oy)+yoffset,mdf*1.01+yoffset,\
scale_y if scale_y else '#',\
axis,title,offset+0.5,offset+ldf/spacing+0.5,\
offset-(offset%xbreaksby),offset+ldf+xbreaksby,xbreaksby,\
scale_x if scale_x else '#',\
-mdf*ltune+oy+yoffset,oy+yoffset,offset+0.5,ldf/spacing+0.5+offset))
if (seqontop):
a.write(
"""+geom_text(aes(x=Resid+%f-0.25,label=seq),hjust=0, vjust=%f)"""
% (offset, -mdf * 0.5))
else:
a.write("""
""")
a.write("""
ggsave("%s",plot=a,height=%f,width=%f,dpi=%d)
""" % (filename if filename[-3:] == 'png' else
(filename + '.png'), 4.0 * htune, 12. / 60. * ldf * wtune, dpi))
a.close()
os.system('R --vanilla --slave < ' +
os.path.join(CONFIG.TEMP_DIR, 'prof4seq.r'))