I plotted a DotPlot following these incredible steps (https://davemcg.github.io/post/lets-plot-scrna-dotplots/) from David but I could only reach the DotPlot part. I tried to calculate and plot the dendrogram and reorder my data, but I didn't succeed.
My code:
> teste2 %>% filter(bacteria %in% markers) %>%
+ ggplot(aes(x = bacteriophage, y = bacteria, color = eop_index, size = virulence_index)) +
+ geom_point() +
+ scale_color_viridis_c(name = 'EOP') +
+ cowplot::theme_cowplot() +
+ theme(axis.line = element_blank()) +
+ theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
+ ylab('') +
+ xlab('') +
+ theme(axis.ticks = element_blank())
My result: DotPlot
What I need: DotPlot that I based my results
It's important to say that the type of data is different. I'm not working with scRNA data, so I'm adapting to my needs. When I apply the same code of David but change the variable names, the result is completely nonsense and does not reorder the data.
The code:
> mat <- teste2 %>%
+ filter(bacteria %in% markers) %>%
+ pivot_wider(names_from = bacteriophage, values_from = eop_index) %>%
+ data.frame() # make df as tibbles -> matrix annoying
> mat <- mat[,-1] #drop gene column as now in rows
> clust <- hclust(dist(mat %>% as.matrix())) # hclust with distance matrix
> ddgram <- as.dendrogram(clust) # create dendrogram
> ggtree_plot <- ggtree::ggtree(ddgram)
> ggtree_plot
> dotplot <- teste2 %>% filter(bacteria %in% markers) %>%
+ mutate(bacteria, factor(bacteria, levels = clust$labels[clust$order])) %>%
+ ggplot(aes(x = bacteriophage, y = bacteria, color = eop_index, size = virulence_index)) +
+ geom_point() +
+ scale_color_viridis_c(name = 'EOP') +
+ cowplot::theme_cowplot() +
+ theme(axis.line = element_blank()) +
+ theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
+ ylab('') +
+ xlab('') +
+ theme(axis.ticks = element_blank())
> plot_grid(ggtree_plot, dotplot, nrow = 1, rel_widths = c(0.5,2), align = 'h')
The result: DotPlot with dendrogram rsrs
Here is a sample of my data: Screenshot of data
If someone could help me, I would appreciate it very much! Thanks in advance!
Obs: I tried to change the variables at different ways, but any of them result a correct dendrogram and reorder the dotplot data sequence.
