Example run
Loading example data from PBMC 3K processed with Seurat (see below for more details).
UMAP coordinates:
## UMAP_1 UMAP_2
## AAACATACAACCAC -4.232792 -4.152139
## AAACATTGAGCTAC -4.892886 10.985685
## AAACATTGATCAGC -5.508639 -7.211088
## AAACCGTGCTTCCG 11.332233 3.161727
## AAACCGTGTATGCG -7.450703 1.092022
## AAACGCACTGGTAC -3.509504 -6.087042Cluster annotations:
## AAACATACAACCAC AAACATTGAGCTAC AAACATTGATCAGC AAACCGTGCTTCCG AAACCGTGTATGCG
## Memory CD4 T B Memory CD4 T CD14+ Mono NK
## AAACGCACTGGTAC
## Memory CD4 T
## 9 Levels: Naive CD4 T Memory CD4 T CD14+ Mono B CD8 T FCGR3A+ Mono NK ... PlateletExpression table for several genes:
## MS4A1 GNLY CD3E CD14 FCER1A FCGR3A
## AAACATACAACCAC -0.4110536 -0.4081782 1.0157094 -0.393789 -0.1373491 -0.4507969
## AAACATTGAGCTAC 2.5965712 -0.4081782 -0.9189074 -0.393789 -0.1373491 -0.4507969
## AAACATTGATCAGC -0.4110536 0.7526607 0.8148764 -0.393789 -0.1373491 -0.4507969
## AAACCGTGCTTCCG -0.4110536 -0.4081782 -0.9189074 -0.393789 -0.1373491 1.1300704
## AAACCGTGTATGCG -0.4110536 2.3958265 -0.9189074 -0.393789 -0.1373491 -0.4507969
## AAACGCACTGGTAC -0.4110536 -0.4081782 1.1029222 -0.393789 -0.1373491 -0.4507969
## LYZ PPBP CD8A
## AAACATACAACCAC -0.11104505 -0.1416271 2.1039769
## AAACATTGAGCTAC 0.06112027 -0.1416271 -0.3537211
## AAACATTGATCAGC 0.07833934 -0.1416271 -0.3537211
## AAACCGTGCTTCCG 1.40875149 2.9255239 -0.3537211
## AAACCGTGTATGCG -0.97272094 -0.1416271 -0.3537211
## AAACGCACTGGTAC -0.06309661 -0.1416271 -0.3537211Let’s plot this data:
data <- data.table(exampleMascarade$dims,
cluster=exampleMascarade$clusters,
exampleMascarade$features)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=cluster)) +
coord_fixed() +
theme_classic()
Now let’s generate cluster masks:
The maskTable is actually a table of cluster borders. A
single cluster can have multiple connected parts, and one a single part
can contain multiple border lines (groups).
## UMAP_1 UMAP_2 part group cluster
## <num> <num> <char> <char> <fctr>
## 1: -3.865697 -8.906611 Memory CD4 T#1 Memory CD4 T#1#1 Memory CD4 T
## 2: -3.831308 -8.895148 Memory CD4 T#1 Memory CD4 T#1#1 Memory CD4 T
## 3: -3.819845 -8.883685 Memory CD4 T#1 Memory CD4 T#1#1 Memory CD4 T
## 4: -3.808383 -8.872222 Memory CD4 T#1 Memory CD4 T#1#1 Memory CD4 T
## 5: -3.796920 -8.860760 Memory CD4 T#1 Memory CD4 T#1#1 Memory CD4 T
## 6: -3.785457 -8.849297 Memory CD4 T#1 Memory CD4 T#1#1 Memory CD4 TNow we can use this table to draw the borders with
geom_path (group column should be used as the
group aesthetics):
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=cluster)) +
geom_path(data=maskTable, aes(group=group)) +
coord_fixed() +
theme_classic()
Or we can color the borders instead of points:
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(color="grey") +
geom_path(data=maskTable, aes(group=group, color=cluster), linewidth=1) +
coord_fixed() +
theme_classic()
We can use ggforce package to make the borders touch
instead of overlap:
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(color="grey") +
ggforce::geom_shape(data=maskTable, aes(group=group, color=cluster),
linewidth=1, fill=NA, expand=unit(-1, "pt")) +
coord_fixed() +
theme_classic()
In the presence of small clusters it can help to expand the borders a bit further away from the points.
maskTable <- generateMask(dims=exampleMascarade$dims,
clusters=exampleMascarade$clusters,
expand=0.02)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(color="grey") +
ggforce::geom_shape(data=maskTable, aes(group=group, color=cluster),
linewidth=1, fill=NA, expand=unit(-1, "pt")) +
coord_fixed() +
theme_classic()
With the help of ggforce we can also put the labels
within the plot itself. For the best results use ggforce
version from https://github.com/assaron/ggforce/tree/remove-offset.
fancyMask <- list(
ggforce::geom_shape(data=maskTable, aes(group=group, color=cluster),
linewidth=1, fill=NA, expand=unit(-1, "pt"), show.legend = FALSE),
ggforce::geom_mark_hull(data=maskTable, fill = NA, aes(group=cluster, color=cluster, label = cluster),
linewidth=0,
radius=0, expand=0, con.cap=0, con.type = "straight",
label.fontsize = 10, label.buffer = unit(0, "cm"),
label.fontface = "plain",
label.minwidth = 0,
label.margin = margin(2, 2, 2, 2, "pt"),
label.lineheight = 0,
con.colour = "inherit",
show.legend = FALSE),
# expanding to give a bit more space for labels
scale_x_continuous(expand = expansion(mult = 0.1)),
scale_y_continuous(expand = expansion(mult = 0.1))
)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(color="grey") +
fancyMask +
coord_fixed() +
theme_classic()
Now we can easily show association between cell types and expression of particular genes, such as GNLY being a good marker for NK cells in this dataset.
library(ggnewscale) # for having two color scales simultaneously
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=GNLY), size=0.5) +
scale_color_gradient2(low = "#404040", high="red") +
new_scale_color() +
fancyMask +
coord_fixed() +
theme_classic()
We can focus on a single cluster too:
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
geom_point(aes(color=GNLY), size=0.5) +
scale_color_gradient2(low = "#404040", high="red") +
geom_path(data=maskTable[cluster=="NK"], aes(group=group)) +
coord_fixed() +
theme_classic()
