Plot gene-by-cell heatmap

Visualize the expressions of the selected features (genes) for all cells/spots.

GCHeatMap(
  obj,
  features,
  cell_label = "Domain",
  fill_legend_title = "Expression",
  do.scale = TRUE,
  grp_label = FALSE,
  pt_size = 4,
  grp_color = NULL,
  ncol.legend = 1,
  legend.position = "right",
  axis_text_y = TRUE,
  y_text_size = 5,
  ...
)

# S3 method for SpatialExperiment
GCHeatMap(
  obj,
  features,
  cell_label = "Domain",
  fill_legend_title = "Expression",
  do.scale = TRUE,
  grp_label = FALSE,
  pt_size = 4,
  grp_color = NULL,
  ncol.legend = 1,
  legend.position = "right",
  axis_text_y = TRUE,
  y_text_size = 5,
  ...
)

Arguments

obj

a SpatialExperiment object.

features

a string vector, a group of selected genes' names.

cell_label

a string, specify name of clusters.

fill_legend_title

a string, the legend title.

do.scale

a logical value, whether scale the gene expression for plot, default as TRUE.

grp_label

a logical value, whether display the cluster labels in plot.

pt_size

a positive real, the point size in plot.

grp_color

a string vector, the colors for each cluster in plot.

ncol.legend

a positive number, the number of columns for legend.

legend.position

a string, the postion of legend.

axis_text_y

a logical value, whether display the tick text in y-axis.

y_text_size

a positive real, the text size for y-axis.

...

other arguments pass to DoHeatmap.

Value

Returns a ggplot object.

Returns a ggplot object.

See also

None