CACIMAR (version 1.0.0)

Plot_MarkersHeatmap: 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

# NOT RUN {
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)])
# }