Shared clonotype abundance plot labels up-side-down.

[suntaosimon]

as figures below,

NonOverlapping should be in grey which is on the top.

looks like it's right in the document sample.

[mikessh]

Hi, can you confirm that your clonotype table have frequencies that 1) sum to 1, 2) are strictly positive?

[suntaosimon]

Yes. They all sum to 1 and positive.

I have tried many data and they all have the same problem in Shared clonotype abundance plot.

Modified the following parts in "intersect_pair_area_v2.r" that seems help,

#dd <- dd[with(dd, order(cdr3nt, levels(dd$cdr3aa))), ]
df.0$cum <- rev(cumsum(rev(df.0$expr)))
df.0$cum <- (c(df.0$cum[-1],0) + df.0$cum) / 2
df.1$cum <- rev(cumsum(rev(df.1$expr)))
df.1$cum <- (c(df.1$cum[-1],0) + df.1$cum) / 2

[tiagobrc]

The very same thing happens to me.

[haojw2815]

830new.paired.strict.table.collapsed.pdf The very same thing happens to me, I Modified the following parts in "intersect_pair_area.r"

#dd <- dd[with(dd, order(cdr3nt, levels(dd$cdr3aa))), ] df.0$cum <- rev(cumsum(rev(df.0$expr))) df.0$cum <- (c(df.0$cum[-1],0) + df.0$cum) / 2 df.1$cum <- rev(cumsum(rev(df.1$expr))) df.1$cum <- (c(df.1$cum[-1],0) + df.1$cum) / 2

But the labels don't match perfect, how to fix it.