Description Usage Arguments Value Examples

Plots a heatmap of gene expression, with cells ordered according to the structure computed by `compute.backbone.tree`

.

1 2 | ```
ct.plot.heatmap(data, b.tree, log.scale = TRUE, sd.filter = 0.7,
reorder.genes = TRUE)
``` |

`data` |
A matrix of (non-negative) RNA-seq expression levels where each row is a gene and each column is the cell sequenced. |

`b.tree` |
igraph object returned by |

`log.scale` |
Boolean (optional). Whether the data should be log-scaled. |

`sd.filter` |
Numeric or |

`reorder.genes` |
Boolean (optional). Whether the gene rows should be reordered using a dendrogram of their mean value. |

`data`

object reordered according to the backbone tree, such as used to plot the heatmap.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
# Load pre-computed LDA model for skeletal myoblast RNA-Seq data from HSMMSingleCell package:
data(HSMM_lda_model)
# Recover sampling time (in days) for each cell:
library(HSMMSingleCell)
data(HSMM_sample_sheet)
days.factor = HSMM_sample_sheet$Hours
days = as.numeric(levels(days.factor))[days.factor]
# Compute near-optimal backbone tree:
b.tree = compute.backbone.tree(HSMM_lda_model, days)
# Plot heatmap:
data(HSMM_expr_matrix)
ct.plot.heatmap(HSMM_expr_matrix[1:2000,], b.tree, reorder.genes=FALSE)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.