plotPca | R Documentation |
Displays the dimensional reduction and maps gene, gene-set or feature information onto the color-aesthetic.
plotPca(
object,
color_by = NULL,
n_pcs = NULL,
method_gs = NULL,
pt_size = NULL,
pt_alpha = NULL,
pt_clrp = NULL,
pt_clrsp = NULL,
pt_clr = NULL,
normalize = NULL,
verbose = NULL,
...
)
plotTsne(
object,
color_by = NULL,
color_aes = "color",
color_trans = "identity",
alpha_by = NULL,
order_by = NULL,
order_desc = FALSE,
pt_shape = 19,
shape_by = NULL,
method_gs = NULL,
pt_size = NULL,
pt_alpha = NULL,
pt_clrsp = NULL,
pt_clrp = NULL,
pt_clr = NULL,
clrp_adjust = NULL,
normalize = NULL,
use_scattermore = FALSE,
sctm_interpolate = FALSE,
sctm_pixels = c(1024, 1024),
verbose = NULL,
...
)
plotTsneComparison(
object,
color_by,
ggpLayers = list(),
display_title = FALSE,
nrow = NULL,
ncol = NULL,
...
)
plotUmap(
object,
color_by = NULL,
color_aes = "color",
color_trans = "identity",
alpha_by = NULL,
order_by = NULL,
order_desc = FALSE,
shape_by = NULL,
method_gs = NULL,
pt_shape = 19,
pt_size = NULL,
pt_alpha = NULL,
pt_clrsp = NULL,
pt_clrp = NULL,
pt_clr = NULL,
clrp_adjust = NULL,
normalize = NULL,
transform_with = list(),
use_scattermore = FALSE,
sctm_interpolate = FALSE,
sctm_pixels = c(1024, 1024),
verbose = NULL,
...
)
plotUmapComparison(
object,
color_by,
ggpLayers = list(),
display_title = FALSE,
nrow = NULL,
ncol = NULL,
...
)
object |
An object of class |
color_by |
The variable to be displayed by color:
|
n_pcs |
Numeric value. Determines the number of principal components to be plotted. Must be an even number. |
method_gs |
Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA(). |
pt_size |
Numeric value. Specifies the size of all points. |
pt_alpha |
Numeric value. Specifies the degree of transparency of all points. |
pt_clrp |
The color palette to be used if the specified variable displayed by
color is categorical/discrete. Run |
pt_clrsp |
The color spectrum to be used if the specified variable displayed by
color is continuous. Run |
pt_clr |
Character value. Specifies the color of all points. |
normalize |
Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded. |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
... |
Used to absorb deprecated arguments or functions. |
order_by |
Character value or |
order_desc |
Logical value. If |
clrp_adjust |
Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group. |
use_scattermore |
Logical value. If |
sctm_interpolate , sctm_pixels |
Given to the corresponding arguments
of |
ggpLayers |
A list of ggplot add ons to add to each plot. |
display_title |
Logical value. If set to TRUE an informative title is displayed. |
nrow , ncol |
Numeric values or NULL. Used to arrange multiple plots. |
transform_with |
List or NULL. If list, can be used to transform continuous variables before plotting.
Names of the list slots refer to the variable. The content of the slot refers to the transforming functions.
Slot content can either be a character vector of function names. Use Useful if you want to apply more than one transformation on variables mapped to
plotting aesthetics. Input for |
The comparison version of each function take a vector of variables
to color by. A list of plots is created that is arranged via grid.arrange()
.
Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.
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