Plot spatial feature heatmaps for a group of SRT data batches

Visualize the gene expressions on spatial coordinates for a group of genes and SRT data batches.

EachExprSpaHeatMap(
  obj,
  features,
  batch = NULL,
  quantVec = NULL,
  combine = TRUE,
  scale = TRUE,
  ...
)

# S3 method for list
EachExprSpaHeatMap(
  obj,
  quantVec = NULL,
  title_name = TRUE,
  combine = TRUE,
  layout.dim = c(round(length(obj[[2]])), ncol(obj[[2]][[1]])),
  no_axis = TRUE,
  pt_size = 1,
  base_size = 10,
  border_col = "gray",
  common.legend = TRUE,
  axis_names = c("Coord x", "Coord y"),
  no_axis_name = TRUE,
  legend.position = "right",
  ...
)

# S3 method for SRTProject
EachExprSpaHeatMap(
  obj,
  features,
  batch = NULL,
  quantVec = NULL,
  combine = TRUE,
  scale = TRUE,
  layout.dim = NULL,
  no_axis = TRUE,
  pt_size = 1,
  base_size = 10,
  border_col = "gray",
  common.legend = TRUE,
  axis_names = c("Coord x", "Coord y"),
  no_axis_name = TRUE,
  legend.position = "right",
  ...
)

Arguments

obj

a SRTProject object.

features

a string vector, a group of genes to be visualized.

batch

a string or positive integer vector, the names or ID of batches to be plotted

quantVec

a real or real vector between 0 and 1, set the midlle scale of continous color schema.

combine

a logical value, whehter put all plots on one figure, default as TRUE.

scale

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

...

other arguments pass to ggarrange.

layout.dim

a 2-diemensional vector, specify the layout (numbers of rows and columns) of figure.

no_axis

a logical value, whether display the axis in plot.

pt_size

a positive real, the point size in plot.

base_size

a positive real, the baseline text size in plot.

border_col

a string, the color of border in plot.

common.legend

a logcial value, whether use a common legend in figure.

axis_names

a 2-dimensional string vector, the axis names in plot.

no_axis_name

a logical value, whether display the axis name in plot.

legend.position

a string, the position of legend.

Value

Returns a ggplot object or a list of ggplot objects.

See also

None.