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This commit is contained in:
Arnar Flatberg 2007-07-24 14:34:47 +00:00
parent 13dc6de5c1
commit 91abf12f51
1 changed files with 17 additions and 4 deletions
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21
scripts/lpls/run_smoker.py
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@ -14,7 +14,7 @@ from plots_lpls import plot_corrloads
# full smoker data # full smoker data
DX = dataset.read_ftsv(open("../../data/smokers-full/Xfull.ftsv")) DX = dataset.read_ftsv(open("../../data/smokers-full/Xfull.ftsv"))
DY = dataset.read_ftsv(open("../../data/smokers-full/Yg.ftsv")) DY = dataset.read_ftsv(open("../../data/smokers-full/Yg.ftsv"))
Y = DY.asarray() Y = DY.asarray().astype('d')
# select subset genes by SAM # select subset genes by SAM
rpy.r.library("siggenes") rpy.r.library("siggenes")
rpy.r.library("qvalue") rpy.r.library("qvalue")
@ -88,7 +88,7 @@ Z, newind = rpy_go.genego_matrix(goterms, tmat, gene_ids, terms,func=mean)
Z = Z.T Z = Z.T
# update X matrix (no go-terms available) # update X matrix (no go-terms available)
Xr = Xr[:,newind] Xr = Xr[:,newind]
gene_ids = asarray(gene_ids)[newind] new_gene_ids = asarray(gene_ids)[newind]
######## LPLSR ######## ######## LPLSR ########
@ -104,6 +104,19 @@ dx,Ry,rssy = correlation_loadings(Y, T, Q)
cadz,Rz,rssz = correlation_loadings(Z.T, W, L) cadz,Rz,rssz = correlation_loadings(Z.T, W, L)
# Prediction error # Prediction error
rmsep , yhat, class_error = cv_lpls(Xr, Y, Z, a_max, alpha=alpha) rmsep , yhat, class_error = cv_lpls(Xr, Y, Z, a_max, alpha=alpha)
alpha_check=False
if alpha_check:
Alpha = arange(0.01, 1, .1)
Rmsep,Yhat, CE = [],[],[]
for a in Alpha:
rmsep , yhat, ce = cv_lpls(Xr, Y, Z, a_max, alpha=alpha)
Rmsep.append(rmsep)
Yhat.append(yhat)
CE.append(yhat)
Rmsep = asarray(Rmsep)
Yhat = asarray(Yhat)
CE = asarray(CE)
# Significance Hotellings T # Significance Hotellings T
Wx, Wz, Wy, = jk_lpls(Xr, Y, Z, aopt) Wx, Wz, Wy, = jk_lpls(Xr, Y, Z, aopt)
@ -119,10 +132,10 @@ bar_col = 'rgb'*5
m = Y.shape[1] m = Y.shape[1]
for a in range(m): for a in range(m):
bar(arange(a_max)+a*bar_w+.1, rmsep[:,a], width=bar_w, color=bar_col[a]) bar(arange(a_max)+a*bar_w+.1, rmsep[:,a], width=bar_w, color=bar_col[a])
ylim([rmsep.min()-.05, rmsep.max()+.05]) ylim([rmsep.min()-.05, rmsep.max()+.05])
title('RMSEP')
figure(2) # Hypoid correlations figure(2) # Hypoid correlations
title('RMSEP')
plot_corrloads(Rz, pc1=0, pc2=1, s=tsqz/10.0, c='b', zorder=5, expvar=evz, ax=None) plot_corrloads(Rz, pc1=0, pc2=1, s=tsqz/10.0, c='b', zorder=5, expvar=evz, ax=None)
ax = gca() ax = gca()
ylabels = DY.get_identifiers('_cat', sorted=True) ylabels = DY.get_identifiers('_cat', sorted=True)