plot_cpdb2 failed plot a chord diagram of cellphonedb results
wzh7768 opened this issue · 3 comments
Dear zktuong,
I'm analyzing scRNA-seq data and using cellPhoneDB. Your ktplots is very useful to visualize CPDB results. Fantastic!
However, "plot_cpdb2" part is hardly worked, could you please help me to find out where I did wrong?
The following shows my code:
interaction_grouping <- read.delim("Interactions_annotation.txt", check.names = FALSE)
sce <- Seurat::as.SingleCellExperiment(CRC_MS)
rowData(sce)$gene_symbols <- row.names(sce)
p <- plot_cpdb2(cell_type1 = 'iCAF',
cell_type2 = 'SPP1+TAM|TREM2+TAM|TREM2+CD168+pTAM',
scdata = sce,
idents = 'labers',
means=means,
pvals=pvalues,
deconvoluted = deconvoluted,
gene_symbol_mapping = 'gene_symbols',
desiredInteractions = list(c('TREM2+TAM','CXCL12+iCAF'),c('TREM2+CD168+pTAM','CXCL12+iCAF'),c('SPP1+TAM','CXCL12+iCAF'),
c('TREM2+TAM','CXCL14+iCAF'),c('TREM2+CD168+pTAM','CXCL14+iCAF'),c('SPP1+TAM','CXCL14+iCAF')),
interaction_grouping = interaction_grouping,
edge_group_colors = c('chemokines'='#e15759','costimulatory'='#59a14f','Th17'='#4e79a7'),
node_group_colors = c('CXCL12+iCAF'='red','CXCL14+iCAF'='hotpink3',
'SPP1+TAM'='deepskyblue','TREM2+CD168+pTAM'='cyan4','TREM2+TAM'='dodgerblue'),
keep_significant_only = T,
standard_scale = T,
remove_self = T
)
The results of p was odd
hi @wzh7768, off the top of my head, i'm wondering if the + in your label names are interferring with the functions internally. Can you check if removing + helps?
Do the other plot_cpdb functions work? like plot_cpdb3 or plot_cpdb4?
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