PlotDoseResponse {synergyfinder} | R Documentation |
A function to visualize the drug combination dose-response data
PlotDoseResponse( data, block_ids = c(1), drugs = c(1, 2), adjusted = TRUE, statistic = NULL, summary_statistic = "mean", high_value_color = "#A90217", low_value_color = "#2166AC", point_color = "#C24B40", curve_color = "black", text_size_scale = 1, heatmap_text_label_size_scale = 1, heatmap_text_label_color = "#000000", curve_plot_title = NULL, heatmap_plot_title = NULL, Emin = NA, Emax = NA, save_file = FALSE, file_type = "pdf", file_name = NULL, width = 12, height = 6 )
data |
A list object generated by function |
block_ids |
A vector of characters/integers or NULL. It contains the
block IDs for the blocks to visualize. By default, it is NULL so that the
visualization of all the drug combinations in input |
drugs |
A vector of characters or integers with length of 2. It contains
the index for two drugs to plot. For example, |
adjusted |
A logical value. If it is |
statistic |
A character or NULL. It indicates the statistics printed in the plot while there are replicates in input data. Available values are:
If it is |
summary_statistic |
A vector of characters or NULL. It indicates the
summary statistics printed in heatmap for all the
If it is |
high_value_color |
An R color value. It indicates the color for the high values. |
low_value_color |
An R color value. It indicates the color for low values. |
point_color |
An R color value. It indicates the color for points in dose response curve plots. |
curve_color |
An R color value. It indicates the color for curves in dose response curve plots. |
text_size_scale |
A numeric value. It is used to control the size of text in the plot. All the text size will multiply by this scale factor. |
heatmap_text_label_size_scale |
A numeric value. It is used to control
the size of text labels in the heatmap plot. It only works while
|
heatmap_text_label_color |
NULL or an R color value. It is used to
control the color of text labels in the heatmap plot. If it is |
curve_plot_title |
A character value to indicate the plot title for the dose-response curve. |
heatmap_plot_title |
A character value to indicate the plot title for the heatmap. |
Emin |
A numeric or |
Emax |
A numeric or |
save_file |
A parameter to specify if the visualization results are saved as pdf files in current working directory or not. If it is FALSE, the results are returned as a list of the plots. It is FALSE by default. |
file_type |
A character. It indicates the format of files you want to save as. Default is "pdf". Available values are "jpeg", "bmp", "png", "tiff", "pdf", "svg". |
file_name |
A character vector. It indicates the file names, if user chose to save the plot to local directory.If it is not defined by user, a default name will be assigned. |
width |
a numeric value. It indicates the width of saved file. |
height |
a numeric value. It indicates the height of saved file. |
A list of plot objects recorded by recordPlot. The
plot will be saved into a local file if save_file = TRUE
. If
save_file = FALSE
, the plot will be printed in default graphic
device.
Shuyu Zheng shuyu.zheng@helsinki.fi
Jing Tang jing.tang@helsinki.fi
## Not run: data("mathews_screening_data") data <- ReshapeData(mathews_screening_data) plots <- PlotDoseResponse(data) ## End(Not run)