Issues visualizing CNV posterior in tSNE embedding using pagoda

[bobbyshih]

Ran numbat successfully and following the published guide for interpreting the results.

I am attempting to visualize CNV posterior in tSNE embedding as below:

pagoda <- readRDS(url('http://pklab.med.harvard.edu/teng/data/con_TNBC1.rds'))
plist = list()
muts  <-  nb$joint_post %>% distinct(seg)
muts <- muts$seg
cnv_type = nb$joint_post %>% distinct(seg, cnv_state) %>% {setNames(.$cnv_state, .$seg)}
for (mut in muts) {
    plist[[mut]] = pagoda$plotEmbedding(
        alpha=0.8,
        size=1, 
        plot.na = F, 
        colors = nb$joint_post %>%
            filter(seg == mut) %>%
            {setNames(.$p_cnv, .$cell)},
        show.legend = T,
        mark.groups = F,
        plot.theme = theme_bw(),
        title = paste0(mut, '(', cnv_type[muts], ')')
    ) +
    scale_color_gradient2(low = 'royalblue', mid = 'white', high = 'red3', midpoint = 0.5, limits = c(0,1), name = 'Posterior')
}
wrap_plots(plist, guides = 'collect')

However I get the following error

Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf

I have run this using the provided example numbat results:

nb_TNBC1= readRDS(url("http://pklab.med.harvard.edu/teng/data/nb_TNBC1.rds"))
plist = list()
muts = c('1a', '3b', '22b')
cnv_type = nb_TNBC1$joint_post %>% distinct(seg, cnv_state) %>% {setNames(.$cnv_state, .$seg)}
for (mut in muts) {
    
    plist[[mut]] = pagoda$plotEmbedding(
        alpha=0.8,
        size=1, 
        plot.na = F, 
        colors = nb_TNBC1$joint_post %>%
            filter(seg == mut) %>%
            {setNames(.$p_cnv, .$cell)},
        show.legend = T,
        mark.groups = F,
        plot.theme = theme_bw(),
        title = paste0(mut, '(', cnv_type[muts], ')')
    ) +
    scale_color_gradient2(low = 'royalblue', mid = 'white', high = 'red3', midpoint = 0.5, limits = c(0,1), name = 'Posterior')
}
wrap_plots(plist, guides = 'collect')

This generates the exact same plots as shown in the guide.

Using my data, if I remove the colors argument the following plot is generated.

pagoda$plotEmbedding(
        alpha=0.8,
        size=1, 
        plot.na = F, 
        show.legend = T,
        mark.groups = F,
        plot.theme = theme_bw()
    )

I have compared the input to colors using both the provided example numbat results as well as mine and can see no difference, so I do not understand why I am getting this error only when using my results.

If it helps I will gladly send over my numbat results, please let me know.

[bobbyshih]

Did not realize I needed to generate my own pagoda object. Fixed itself!

[christophechu]

@bobbyshih How to generate own pagoda object?