Create a Data Frame Suitable for ggplot()

Source: R/assay.R

Generate a long-format data frame for ease of use with ggplot(); as a bonus, this method enables direct calling of Assay objects in ggplot() (see examples)

# S3 method for Assay
fortify(
  model,
  data,
  features = NULL,
  layer = c("data", "scale.data", "counts"),
  na.rm = FALSE,
  ...
)

Arguments

model

An Assay object

data

A data.frame (eg. from FetchData) with extra data for visualization

features

A vector of features to include in the fortified data; defaults to the variable features

layer

Name of layer to pull expression data for

na.rm

Remove values with NAs

...

Ignored

Value

A long-format data frame for use with ggplot()

Details

fortify.Assay() generates a data frame based on the expression data stored in layer; automatically creates a column for cell names (“cell”). Also creates creates a column for identity classes (“ident”) if not present in data; the default identity class is “SeuratProject” ; final column output order is:

  • “cell”

  • “ident”

  • expression data for features

  • additional meta data provided by data

See also

ggplot2::ggplot(), ggplot2::fortify()

Visualize Assay Expression Data: autolayer.Assay(), autoplot.Assay()

Examples

data("pbmc_small")
rna <- pbmc_small[["RNA"]]
md <- FetchData(pbmc_small, vars = "ident")

# Create a data frame for `ggplot()`
df <- fortify(rna, data = md)
head(df)
#>             cell ident     PPBP IGLL5    VDAC3 CD1C AKR1C3 PF4 MYL9     GNLY
#> 1 ATGCCAGAACGACT     0 0.000000     0 0.000000    0      0   0    0 0.000000
#> 2 CATGGCCTGTGCAT     0 0.000000     0 0.000000    0      0   0    0 0.000000
#> 3 GAACCTGATGAACC     0 4.753095     0 0.000000    0      0   0    0 0.000000
#> 4 TGACTGGATTCTCA     0 0.000000     0 4.378773    0      0   0    0 4.378773
#> 5 AGTCAGACTGCACA     0 0.000000     0 0.000000    0      0   0    0 0.000000
#> 6 TCTGATACACGTGT     0 0.000000     0 0.000000    0      0   0    0 0.000000
#>   TREML1 CA2 SDPR PGRMC1 S100A8    TUBB1 HLA-DQA1 PARVB RUFY1 HLA-DPB1
#> 1      0   0    0      0      0 0.000000 0.000000     0     0        0
#> 2      0   0    0      0      0 4.776153 0.000000     0     0        0
#> 3      0   0    0      0      0 0.000000 0.000000     0     0        0
#> 4      0   0    0      0      0 0.000000 4.378773     0     0        0
#> 5      0   0    0      0      0 0.000000 0.000000     0     0        0
#> 6      0   0    0      0      0 0.000000 0.000000     0     0        0
#>   RP11-290F20.3   S100A9
#> 1      0.000000 0.000000
#> 2      0.000000 4.776153
#> 3      4.753095 4.753095
#> 4      0.000000 0.000000
#> 5      0.000000 0.000000
#> 6      0.000000 0.000000
ggplot(df, mapping = aes(x = ident, y = PPBP, fill = ident)) +
  geom_violin()


# Use an `Assay` directly in `ggplot()`
ggplot(rna, mapping = aes(x = ident, y = GNLY, fill = ident), md) +
  geom_violin()