Commit 10badf91 authored by Carine Rey's avatar Carine Rey
Browse files

get more info from simus

parent e51ad99e
...@@ -170,6 +170,8 @@ for leaf in NonConvLeaves: ...@@ -170,6 +170,8 @@ for leaf in NonConvLeaves:
ConvAA_l = [0] * n_sites #A = nb AA in ConvLeaves
NonConvAA_l = [0] * n_sites #A = nb AA in NonConvLeaves
OnlyConvAA = [0] * n_sites #A = nb AA only in ConvLeaves OnlyConvAA = [0] * n_sites #A = nb AA only in ConvLeaves
OnlyNonConvAA = [0] * n_sites #C = nb AA only in NonConvLeaves OnlyNonConvAA = [0] * n_sites #C = nb AA only in NonConvLeaves
OnlyNonConv_ConvAA = [0] * n_sites #B = nb AA only in (NonConvLeaves AND ConvLeaves) OnlyNonConv_ConvAA = [0] * n_sites #B = nb AA only in (NonConvLeaves AND ConvLeaves)
...@@ -183,16 +185,20 @@ for i in range(n_sites): ...@@ -183,16 +185,20 @@ for i in range(n_sites):
logger.debug(NonConv_AA_per_site_l[i]) logger.debug(NonConv_AA_per_site_l[i])
logger.debug(NonConvAA) logger.debug(NonConvAA)
ConvAA_l[i] = len(ConvAA)
NonConvAA_l[i] = len(NonConvAA)
OnlyConvAA[i] = len(ConvAA - NonConvAA) OnlyConvAA[i] = len(ConvAA - NonConvAA)
OnlyNonConvAA[i] = len(NonConvAA - ConvAA) OnlyNonConvAA[i] = len(NonConvAA - ConvAA)
OnlyNonConv_ConvAA[i] = len(ConvAA.intersection(NonConvAA)) OnlyNonConv_ConvAA[i] = len(ConvAA.intersection(NonConvAA))
df_final = pd.DataFrame({'Sites': Sites, df_final = pd.DataFrame({'Sites': Sites,
'NbConvAA' : ConvAA_l,
'NbNonConvAA' : NonConvAA_l,
'NbOnlyConvAA' : OnlyConvAA, 'NbOnlyConvAA' : OnlyConvAA,
'NbOnlyNonConvAA' : OnlyNonConvAA, 'NbOnlyNonConvAA' : OnlyNonConvAA,
'NbCommonAA' : OnlyNonConv_ConvAA}) 'NbCommonAA' : OnlyNonConv_ConvAA})
df_final = df_final[["Sites","NbOnlyConvAA","NbOnlyNonConvAA","NbCommonAA"]] df_final = df_final[["Sites","NbConvAA","NbNonConvAA","NbOnlyConvAA","NbOnlyNonConvAA","NbCommonAA"]]
#=================================================================================================== #===================================================================================================
# Read profile info per site table # Read profile info per site table
......
...@@ -68,14 +68,30 @@ plotC = ggplot(df, aes(x=NbOnlyNonConvAA, fill=hyp)) + theme_bw() + labs(x=x_lab ...@@ -68,14 +68,30 @@ plotC = ggplot(df, aes(x=NbOnlyNonConvAA, fill=hyp)) + theme_bw() + labs(x=x_lab
plotC = plotC + geom_histogram(binwidth = 0.05) plotC = plotC + geom_histogram(binwidth = 0.05)
plotC = plotC + facet_grid(hyp ~ tree) plotC = plotC + facet_grid(hyp ~ tree)
plot_all <- plot_grid(plotA, plotB, plotC, alpha = 0.7
labels=c("AUTO"), nrow = 3) x_labs = " # of AA in ConvLeaves"
y_labs = "# of sites"
plotD = ggplot(df, aes(x=NbConvAA, fill=hyp)) + theme_bw() + labs(x=x_labs, y=y_labs)
plotD = plotD + geom_histogram(binwidth = 0.05)
plotD = plotD + facet_grid(hyp ~ tree)
alpha = 0.7
x_labs = " # of AA in NonConvLeaves"
y_labs = "# of sites"
plotE = ggplot(df, aes(x=NbnonConvAA, fill=hyp)) + theme_bw() + labs(x=x_labs, y=y_labs)
plotE = plotE + geom_histogram(binwidth = 0.05)
plotE = plotE + facet_grid(hyp ~ tree)
plot_all <- plot_grid(plotA, plotB, plotC, plotD, plotE,
labels=c("AUTO"), nrow = 5)
output_pdf = paste0(opt$out,".pdf") output_pdf = paste0(opt$out,".pdf")
save_plot(output_pdf, save_plot(output_pdf,
plot_all, plot_all,
ncol = 0.8 * length(unique(df$tree)), ncol = 0.8 * length(unique(df$tree)),
nrow = 0.35 * length(unique(df$hyp)) * 3, nrow = 0.35 * length(unique(df$hyp)) * 5,
base_aspect_ratio = 2, base_aspect_ratio = 2,
limitsize = FALSE limitsize = FALSE
) )
......
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