冲积地块未显示通量

Question

i would like to create an alluvial plot that shows the flux of cells between two condition. I was using data from metadata seurat object.

my data:

 meta= data.frame(cell= rownames(seurat@meta.data), geno= seurat$genotype, cluster= seurat$seurat_cluster, num= 1:length(rownames(seurat@meta.data)))


head(meta)
                                                   cell  geno cluster num
KO_d8_r1_AAACAGCCAACCCTAA-1 KO_d8_r1_AAACAGCCAACCCTAA-1 KO_d8       6   1
KO_d8_r1_AAACAGCCAGGAACAT-1 KO_d8_r1_AAACAGCCAGGAACAT-1 KO_d8       1   2
KO_d8_r1_AAACAGCCATGTTGCA-1 KO_d8_r1_AAACAGCCATGTTGCA-1 KO_d8       1   3
KO_d8_r1_AAACATGCATAGCGGA-1 KO_d8_r1_AAACATGCATAGCGGA-1 KO_d8       1   4
KO_d8_r1_AAACCAACATGGCCTG-1 KO_d8_r1_AAACCAACATGGCCTG-1 KO_d8       3   5
KO_d8_r1_AAACCGAAGGGCTTAT-1 KO_d8_r1_AAACCGAAGGGCTTAT-1 KO_d8       5   6
 
tail(meta)
                                                       cell  geno cluster  num
    WT_d8_r2_TTTGTCCCAATCCCTT-1 WT_d8_r2_TTTGTCCCAATCCCTT-1 WT_d8       4 6598
    WT_d8_r2_TTTGTCTAGGATCACT-1 WT_d8_r2_TTTGTCTAGGATCACT-1 WT_d8       5 6599
    WT_d8_r2_TTTGTGAAGTTAGAGG-1 WT_d8_r2_TTTGTGAAGTTAGAGG-1 WT_d8       1 6600
    WT_d8_r2_TTTGTGGCACAACCTA-1 WT_d8_r2_TTTGTGGCACAACCTA-1 WT_d8       6 6601
    WT_d8_r2_TTTGTGTTCCTTGAGG-1 WT_d8_r2_TTTGTGTTCCTTGAGG-1 WT_d8       0 6602
    WT_d8_r2_TTTGTTGGTAGCCTAA-1 WT_d8_r2_TTTGTTGGTAGCCTAA-1 WT_d8       4 6603

my code:

ggplot(meta,
       aes(x = geno, stratum = cluster, alluvium = num, y = cluster,
           fill = num, label = cluster)) +
  scale_x_discrete(expand = c(.1, 0)) +
  geom_flow(width = 1/4) +
  geom_stratum(alpha = .5, width = 1/4) +
  geom_text(stat = "stratum", size = 4) +
  theme(legend.position = "none") +
  ggtitle("flux of cells")

my output:

But the alluvial plot, as you see, don't show the flux of cells. any suggestions?

Answer 1

Introduction

I think the issue you are facing is more on how to define the alluvium parameter. This parameter should relate to the flow of information between the right and the left stratum. So, it should define the alluvium category for every row of your data. For example, one category could be the alluvial (flow) between cluster 0 in “KO_d8” and cluster 1 in “WT_d8”. Here it seems that the num column (used to define the alluvium) does not represent the alluvium.

In the data represented, I do not see what is the link between the two stratums, ie what associates the lines (or cells;) ) belonging in the “KO_d8” genotype and the ones in the “WT_d8” genotype.

Knowing this, there can only be two cases:

1. There really is a link between cells in “KO_d8” and the ones in the “WT_d8”
2. There is no link between cells in “KO_d8” and the ones in the “WT_d8”

Case n°1:

In that case, you have to find the column defining the link between the cells in the two categories. Then, you may replicate the long-form alluvium as described in the ggalluvial vignette ( link ).

Case n°2:

In that case, I imagine that you only want to visualize how the intra-proportion of clusters change in the two stratum conditions.

Here, the alluvium links only the cluster n° x in stratum “KO_d8” to the same cluster n° x in stratum “WT_d8”. For x ranging from 0 to 13 .

For this you need to process your data in the correct format.

# Load library for data transformation
library(dplyr)

# Count the number of cells per `geno`
geno.smry <- table(meta$geno)

# Get the number of cells per `cluster` and per `geno`
meta.2.plot <- meta %>% 
  dplyr::group_by(cluster, geno) %>%
  dplyr::summarise(n_cells = n())

# Get the fraction of cells per `cluster` for each `geno`
meta.2.plot$n_cells_tot_per_geno <- as.numeric(geno.smry[meta.2.plot$geno])
meta.2.plot$fraction_cells <- meta.2.plot$n_cells / meta.2.plot$n_cells_per_geno

So that you can plot the alluvial as:

# Plot the alluvial
ggplot(meta.2.plot,
       aes(x = geno, y = fraction_cells,
           stratum = cluster, alluvium = cluster,
           fill = cluster, label = cluster)) +
  scale_x_discrete(expand = c(.1, 0)) +
  geom_flow(width = 1/4) +
  geom_stratum(alpha = .5, width = 1/4) +
  geom_text(stat = "stratum", size = 4) +
  theme(legend.position = "none") +
  ggtitle("flux of cells")