Plot_MarkersHeatmap: Plot Markers in each cell type

In CACIMAR: Cross-Species Analysis of Cell Identities, Markers and Regulations

Plot Markers in each cell type

Description

This function integrate R package pheatmap to plot markers in each cell type

Usage

Plot_MarkersHeatmap(
  ConservedMarker,
  start_col = 2,
  module_colors = NA,
  heatmap_colors = NA,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  show_rownames = FALSE,
  show_colnames = FALSE,
  cellwidth = NA,
  cellheight = NA,
  legend = FALSE,
  annotation_legend = FALSE,
  annotation_names_row = FALSE,
  ...
)

Arguments

ConservedMarker	Markers table
start_col	numeric, indicating the start column of marker power in each cell type
module_colors	vector, indicating colors of modules (annotation_colors)
heatmap_colors	vector, indicating colors used in heatmap
cluster_rows	boolean values determining if rows should be clustered or hclust object
cluster_cols	boolean values determining if columns should be clustered or hclust object
show_rownames	boolean specifying if column names are be shown
show_colnames	boolean specifying if column names are be shown
cellwidth	individual cell width in points. If left as NA, then the values depend on the size of plotting window
cellheight	individual cell height in points. If left as NA, then the values depend on the size of plotting window
legend	logical to determine if legend should be drawn or not
annotation_legend	boolean value showing if the legend for annotation tracks should be drawn
annotation_names_row	boolean value showing if the names for row annotation tracks should be drawn
...	parameter in pheatmap

Value

pheatmap object

Examples

data("pbmc_small")
all.markers <- Identify_Markers(pbmc_small)
all.markers <- Format_Markers_Frac(all.markers)
Plot_MarkersHeatmap(all.markers[,c(2,6,7,8)])

CACIMAR documentation built on May 18, 2022, 9:07 a.m.