plotInfReps | R Documentation |

For datasets with inferential replicates, boxplots are
drawn for the two groups and potentially grouped by
covariates. For datasets with only mean and variance,
points and intervals (95
approximation) are drawn. Additionally, for numeric
`x`

values, points and intervals will be drawn
and `computeInfRV`

should be run first
in order to add the mean and variance statistics.

```
plotInfReps(
y,
idx,
x,
cov = NULL,
colsDrk = c("dodgerblue", "goldenrod4", "royalblue4", "red3", "purple4", "darkgreen"),
colsLgt = c("lightblue1", "goldenrod1", "royalblue1", "salmon1", "orchid1",
"limegreen"),
xaxis,
xlab,
ylim,
main,
mainCol,
legend = FALSE,
legendPos = "topleft",
legendTitle = FALSE,
legendCex = 1,
useMean = TRUE,
q = qnorm(0.975),
applySF = FALSE,
reorder,
thin,
shiftX
)
```

`y` |
a SummarizedExperiment (see |

`idx` |
the name or row number of the gene or transcript |

`x` |
the name of the condition variable for splitting
and coloring the samples or cells. Also can be a numeric,
e.g. pseudotime, in which case, |

`cov` |
the name of the covariate for adjustment |

`colsDrk` |
dark colors for the lines of the boxes |

`colsLgt` |
light colors for the inside of the boxes |

`xaxis` |
logical, whether to label the sample numbers.
default is |

`xlab` |
the x-axis label |

`ylim` |
y limits |

`main` |
title |

`mainCol` |
name of metadata column to use for title (instead of rowname) |

`legend` |
logical, show simple legend (default FALSE) |

`legendPos` |
character, position of the legend (default "topleft") |

`legendTitle` |
logical, whether to add the name of the grouping variable as a title on the legend (default FALSE) |

`legendCex` |
numeric, size of the legend (default 1) |

`useMean` |
logical, when inferential replicates
are not present or when |

`q` |
numeric, the quantile to use when plotting
the intervals when inferential replicates are not
present or when |

`applySF` |
logical, when inferential replicates are
not present, should |

`reorder` |
logical, should points within a group defined by condition and covariate be re-ordered by their count value (default is FALSE, except for alevin data) |

`thin` |
integer, should the mean and interval lines be drawn thin (the default switches from 0 [not thin] to 1 [thinner] at n=150 cells, and from 1 [thinner] to 2 [thinnest] at n=400 cells) |

`shiftX` |
when |

nothing, a plot is displayed

```
y <- makeSimSwishData()
plotInfReps(y, 3, "condition")
y <- makeSimSwishData(n=40)
y$batch <- factor(rep(c(1,2,3,1,2,3),c(5,10,5,5,10,5)))
plotInfReps(y, 3, "condition", "batch")
```

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