View source: R/imprints_barplotting_app.R
imprints_barplotting_app | R Documentation |
Function to generate IMPRINTS bar plot and pdf file with multipanel bar plots for IMPRINTS-CETSA data. This function is based on the function imprints_barplotting from the IMPRINTS.CETSA package.
imprints_barplotting_app(
data,
treatmentlevel = get_treat_level(data),
setlevel = NULL,
printBothName = TRUE,
printGeneName = FALSE,
witherrorbar = TRUE,
withpoint = FALSE,
pointperrep = TRUE,
layout = NULL,
colorpanel = PaletteWithoutGrey(treatmentlevel),
usegradient = FALSE,
colorgradient = c("#4575B4", "ivory", "#D73027"),
linegraph = FALSE,
log2scale = TRUE,
ratio = 0.6,
ret_plot = TRUE,
save_pdf = FALSE,
toplabel = "IMPRINTS-CETSA bar plotting",
leftlabel = "",
bottomlabel = "",
pdfname = "barplot",
pdfheight = 12,
pdfwidth = 12
)
data |
dataset after imprints_caldiff to plot. Can also be a list of this dataset. |
treatmentlevel |
a vector of treatment labels, such as c("DMSO","TNFa","AT26533") the order determines the arrangement, so in this case DMSO group would be the first group |
setlevel |
a vector of set information if any, such as c("M13","M16") |
printBothName |
A logical to tell if you want to print the both protein names on the plot |
printGeneName |
A logical to tell if you want to print the gene names on the plot |
witherrorbar |
A logical to print or not the error bar on the plot |
withpoint |
A logical to print or not the data point of each replicate on the plot on top of the bars |
pointperrep |
A logical to separate the point per replicate; only active when withpoint is set to TRUE |
layout |
a vector indicating the panel layout for multi-panel plots per page, default value is c(2,3) for set containing data, otherwise c(4,3), use when save_pdf = TRUE |
colorpanel |
a vector of color scheme provided by default with the function PaletteWithoutGrey |
usegradient |
whether the barplot should be draw in color gradient format |
colorgradient |
the color scheme of gradient applied, default value c("#4575B4","ivory", "#D73027") |
linegraph |
whether to plot the graph in a line graph format, default set to FALSE |
log2scale |
whether the yscales should be in log2 scale, default set to TRUE |
ratio |
aspect ratio of the plot, default set to 0.6 |
ret_plot |
Logical to tell if you want to return the last plot |
save_pdf |
A logical to tell if you want to save plots in a pdf file |
toplabel |
textual label at the top part of the page |
leftlabel |
textual label at the left side of the page |
bottomlabel |
textual label at the bottom part of the page |
pdfname |
textual label of the pdf file |
pdfheight |
a number indicate the height of pdf file, default value 12 |
pdfwidth |
a number indicate the width of pdf file, default value 12 |
The imprints barplot
imprints_barplotting
library(IMPRINTS.CETSA)
library(IMPRINTS.CETSA.app)
elutriation_wVeh <- elutriation[,-grep("G1",names(elutriation))]
O43776_elu <- elutriation_wVeh[which(elutriation_wVeh$id == "O43776"),]
imprints_barplotting_app(O43776_elu)
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