I am trying to create a ggplot from a list column. First I create the list column and then the ggplot. The intended ggplot is a ggupset to show set intersections. I followed the ggupset example to create the list column and plot. However, I get the following warning when trying to create a geom_bar()
from the list column: Warning message: Computation failed in stat_count():non-numeric argument to mathematical function
. I am also unable to reproduce the ggupset example using tidy_pathway_member
. Below is a simple reprex as well as the ggupset example.
Thank you for your time and help!
library(dplyr)
library(tidyr)
library(ggplot2)
library(ggupset)
# Simple reprex
df <-
dplyr::tribble(
~id, ~color,
"a", "red",
"b", "blue",
"b", "purple",
"c", "purple",
"d", "red",
"d", "blue"
)
df_list_col <-
df %>%
group_by(id) %>%
summarise(colors = list(color))
#> `summarise()` ungrouping output (override with `.groups` argument)
# ggplot fails
# desired output is a bar graph with each intersection of categories on x-axis (i.e., "red", "blue,purple", "purple", "red,blue")
df_list_col %>%
ggplot(aes(x = colors)) +
geom_bar() #+
#> Warning: Computation failed in `stat_count()`:
#> non-numeric argument to mathematical function
# ggupset::scale_x_upset()
# Reproduce example taken from `ggupset` (https://github.com/const-ae/ggupset)
tidy_pathway_member <-
ggupset::gene_pathway_membership %>%
as_tibble(rownames = "Pathway") %>%
tidyr::gather(Gene, Member, -Pathway) %>%
filter(Member) %>%
select(- Member)
tidy_pathway_member_list_col <-
tidy_pathway_member %>%
group_by(Gene) %>%
summarize(Pathways = list(Pathway))
#> `summarise()` ungrouping output (override with `.groups` argument)
# ggplot fails
# desired output available at https://github.com/const-ae/ggupset under "Reshaping quadratic data"
tidy_pathway_member_list_col %>%
ggplot(aes(x = Pathways)) +
geom_bar() #+
#> Warning: Computation failed in `stat_count()`:
#> non-numeric argument to mathematical function
# ggupset::scale_x_upset()
Created on 2021-01-05 by the reprex package (v0.3.0)
Because you've commented out + scale_x_upset()
, the regular ggplot2 scales don't recognize list-columns as something that can map to a scale. If you un-comment the upset scales, it works as I would expect:
library(dplyr)
library(tidyr)
library(ggplot2)
library(ggupset)
# Simple reprex
df <-
dplyr::tribble(
~id, ~color,
"a", "red",
"b", "blue",
"b", "purple",
"c", "purple",
"d", "red",
"d", "blue"
)
df_list_col <-
df %>%
group_by(id) %>%
summarise(colors = list(color))
#> `summarise()` ungrouping output (override with `.groups` argument)
df_list_col %>%
ggplot(aes(x = colors)) +
geom_bar() +
scale_x_upset()
Created on 2021-01-05 by the reprex package (v0.3.0)