generates an amino acid by position heatmap for input dataset and given column (derived from Rosace scoreHeatmap function)
Usage
lilace_score_heatmap(
data,
savedir,
ctrl.name = "synonymous",
pos.col = "position",
wt.col = "wildtype",
mut.col = "mutation",
type.col = "type",
score.col = "mean",
aa.order = NA,
npos = 100,
ncol = 1,
pos.step = 5,
x.text = 6,
y.text = 3,
seq.text = 1.1,
c.pallete = "RdBu",
c.scale = list(),
ht = 11,
wd = 8.5,
name = "Heatmap",
savepdf = TRUE,
savesvg = FALSE,
show = FALSE,
factor_score = FALSE,
discovery_score = FALSE,
compare_score = FALSE,
category_score = FALSE,
cat_name = "discovery"
)Arguments
- data
Scores data frame. Expected to have columns containing information about position, control amino acid, mutated amino acid, mutation type, and score.
- savedir
Character string specifying the directory to save plots.
- ctrl.name
String specifying the control mutation name. Default is `synonymous`.
- pos.col
Column name in `data` for mutation positions. Default is `position`.
- wt.col
Column name in `data` for wildtype amino acids. Default is `wildtype`.
- mut.col
Column name in `data` for mutated amino acids. Default is `mutation`.
- type.col
Column name in `data` for mutation types. Default is `type`.
- score.col
Column name in `data` for mutation scores. Default is `mean`.
- aa.order
Character vector defining the order of amino acid mutations in the y-axis. Default to using mutations from `data` in alphabetical order.
- npos
Integer specifying the number of positions per subplot. Default is `100`.
- ncol
Integer specifying the number of columns of subplots. Default is `1`.
- pos.step
Integer specifying the steps between x-axis labels. Default is `5`.
- x.text
Numeric value for x-axis text size. Default is `6`.
- y.text
Numeric value for y-axis text size. Default is `3`.
- seq.text
Numeric value for wildtype sequence text size. Default is `1.1`
- c.pallete
Character string or vector defining the color palette. Default is `'RdBu'`.
- c.scale
List of parameters definning the score color scale.
- ht
Numeric value for the height of the saved plot. Default is `11`.
- wd
Numeric value for the width of the saved plot. Default is `8.5`.
- name
Character string specifying the base name of the saved file.
- savepdf
Logical indicating whether to also save a PDF version of the plot. Default is `TRUE`.
- savesvg
Logical indicating whether to also save a SVG version of the plot. Default is `TRUE`.
- show
Logical indicating whether or not to display the plot in the viewer. Default is `FALSE`.
- factor_score
boolean for plotting factor variable with up to 6 levels
- discovery_score
boolean for plotting vector with "LOF", "Not significant", and "GOF" labels
- compare_score
boolean for plotting labels with format "<+/-/=><GOF/LOF>" or "agree" to compare discoveries
- category_score
boolean for plotting score column as factor
- cat_name
name of category plotted in factor_score, discovery_score, or compare_score