corybrunson
commented
4 years ago Hi @mimisikai, thanks for raising the issue, and i think i have the solution. The code below first reproduces your example after reconstructing the data, then uses the aes.bind parameter of stat_alluvium() to rearrange the lodes within each stratum so that those with the same aesthetics (in this case only fill) are adjacent, before they are rearranged according to the default rules. Is this the plot you wanted?
In case you're not familiar with ggplot2 internals: Whenever a layer is produced by a stat or a geom, parameters can be passed to either the stat or geom itself or the geom or stat (respectively) that it is paired with. geom_alluvium() pairs with stat_alluvium() by default, so, when the geom fails to recognize the aes.bind parameter, it passes this parameter to the stat instead. The parameter is documented there, at help(stat_alluvium).
# default alluvium settings
ggplot(data = data,
aes(axis1 = TP1, axis2 = TP2, axis3 = TP3,
y = Freq)) +
scale_x_discrete(limits = c("TP1", "TP2", "TP3"), expand = c(.1, .05)) +
xlab("Time point") +
geom_alluvium(aes(fill = V)) +
geom_stratum() + geom_text(stat = "stratum", infer.label = TRUE) +
theme_minimal()
# bind by aesthetics
ggplot(data = data,
aes(axis1 = TP1, axis2 = TP2, axis3 = TP3,
y = Freq)) +
scale_x_discrete(limits = c("TP1", "TP2", "TP3"), expand = c(.1, .05)) +
xlab("Time point") +
geom_alluvium(aes(fill = V), aes.bind = "alluvia") +
geom_stratum() + geom_text(stat = "stratum", infer.label = TRUE) +
theme_minimal()
Created on 2020-04-02 by the reprex package (v0.3.0)
joe-jhou2
mbojan
I've mock example like
TP1, TP2, TP3 are time points. Beside TP1, TP2 has two "segments", D1D1, D1D2, TP3 has four "segments" D1D1D1, D1D1D2, D1D2D1 and D1D2D2.
The plot I made like this:
ggplot(data = data, aes(axis1 = TP1, axis2 = TP2, axis3 = TP3, y = Freq)) + scale_x_discrete(limits = c("TP1", "TP2", "TP3"), expand = c(.1, .05)) + xlab("Time point") + geom_alluvium(aes(fill = V)) + geom_stratum() + geom_text(stat = "stratum", infer.label = TRUE) + theme_minimal()
What I desired, for example, TP1, only one segment D1 is there, I want it won't split too many substreams for the downstream. e.g. IGHV1 only shows once at TP1 and split into two for TP2(D1D1 and D1D2).