May 14, May 9, Apr 25, Apr 17, Apr 10, Mar 30, Mar 12, Download the file for your platform. If you're not sure which to choose, learn more about installing packages. Warning Some features may not work without JavaScript. Please try enabling it if you encounter problems. Search PyPI Search. Latest version Released: Nov 21, Bioinformatics data analysis and visualization toolkit. Navigation Project description Release history Download files.
Project links Homepage. Maintainers renpy. Project description Project details Release history Download files Project description The bioinfokit toolkit aimed to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments. This is necessary for plotting gene label on the points [string][default: None] genenames Tuple of gene Ids to label the points.
The gene Ids must be present in the geneid column. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] axtickfontsize Font size for axis ticks [float][default: 9] axtickfontname Font name for axis ticks [string][default: 'Arial'] axlabelfontsize Font size for axis labels [float][default: 9] axlabelfontname Font name for axis labels [string][default: 'Arial'] axxlabel Label for X-axis.
If you provide this option, default label will be replaced [string][default: None] axylabel Label for Y-axis. If you provide this option, default label will be replaced [string][default: None] xlm Range of ticks to plot on X-axis [float left, right, interval ][default: None] ylm Range of ticks to plot on Y-axis [float bottom, top, interval ][default: None] plotlegend plot legend on volcano plot [True or False][default:False] legendpos position of the legend on plot.
If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']] theme Change background theme. If theme set to dark , the dark background will be produced instead of white [string][default:'None'] Returns: Volcano plot image in same directory volcano. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] show Show the figure on console instead of saving in current folder [True or False][default:False] axxlabel Label for X-axis.
If you provide this option, default label will be replaced [string][default: None] axlabelfontsize Font size for axis labels [float][default: 9] axtickfontsize Font size for axis ticks [float][default: 9] axtickfontname Font name for axis ticks [string][default: 'Arial'] plotlegend plot legend on inverted volcano plot [True or False][default:False] legendpos position of the legend on plot. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']] ar Rotation of X and Y-axis ticks labels [float][default: 90] theme Change background theme.
If theme set to dark , the dark background will be produced instead of white [string][default:'None'] Returns: Inverted volcano plot image in same directory involcano.
If you provide this option, default label will be replaced [string][default: None] axlabelfontsize Font size for axis labels [float][default: 9] axtickfontsize Font size for axis ticks [float][default: 9] axtickfontname Font name for axis ticks [string][default: 'Arial'] xlm Range of ticks to plot on X-axis [float left, right, interval ][default: None] ylm Range of ticks to plot on Y-axis [float bottom, top, interval ][default: None] fclines draw log fold change threshold lines as defines by lfc [True or False][default:False] fclinescolor color of fclines [string][default: ' a4'] plotlegend plot legend on MA plot [True or False][default:False] legendpos position of the legend on plot.
See more themes here [string][default:'None'] geneid Name of a column having gene Ids. It should not have NA or missing values cmap Color Palette for heatmap [string][default: 'seismic'] scale Draw a color key with heatmap [boolean True or False ][default: True] dim heatmap figure size [ Tuple of two floats width, height in inches][default: 6, 8 ] rowclus Draw hierarchical clustering for rows [boolean True or False ][default: True] colclus Draw hierarchical clustering for columns [boolean True or False ][default: True] zscore Z-score standardization of row 0 or column 1.
It works when clus is True. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] figname name of figure [string ][default:"heatmap"] theme Change background theme.
If theme set to dark , the dark background will be produced instead of white [string][default:'None'] Returns: heatmap plot heatmap. If you provide this option, default label will be replaced [string][default: None] figtype Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] r Figure resolution in dpi [int][default: ] show Show the figure on console instead of saving in current folder [True or False][default:False] dim Figure size [ Tuple of two floats width, height in inches][default: 6, 4 ] theme Change background theme.
If theme set to dark , the dark background will be produced instead of white [string][default:'None'] Returns: Scree plot image screeplot. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] r Figure resolution in dpi [int][default: ] show Show the figure on console instead of saving in current folder [True or False][default:False] plotlabels Plot labels as defined by labels parameter [True or False][default:True] dim Figure size [ Tuple of two floats width, height in inches][default: 6, 4 ] theme Change background theme.
Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] r Figure resolution in dpi [int][default: ] show Show the figure on console instead of saving in current folder [True or False][default:False] markerdot Shape of the dot on plot.
Genes with missing expression values NA will be dropped. Genes with missing expression or gene length values NA will be dropped. If set to False , the original values in pv will be used. This is useful in case of Fst values. It can accept two alternate colors or the number colors equal to chromosome number. Additionally, it also accepts the dict of SNPs and its associated gene name.
If this option set to True, it will label all SNPs with P-value significant score defined by gwasp [string, list, Tuple , dict][default: True] gfont Font size for SNP names to display on the plot [float][default: 8]. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] show Show the figure on console instead of saving in current folder [Boolean True or False ][default:False] axxlabel Label for X-axis.
If you provide this option, default label will be replaced [string][default: None] axlabelfontsize Font size for axis labels [float][default: 9] ylm Range of ticks to plot on Y-axis [float Tuple bottom, top, interval ][default: None] gstyle Style of the text for markernames.
If theme set to dark , the dark background will be produced instead of white [string][default:'None'] Returns: Manhattan plot image in same directory Manhattan. All accession must be separated by a newline in the file. You can get a detailed option for fasterq-dump using the -help option. Note yet defined. IDs must be separated by newline. Ideally, you should have three or more variables. Dataframe should not have identifier column. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] axtickfontsize Font size for axis ticks [float][default: 7] axtickfontname Font name for axis ticks [string][default: 'Arial'] theme Change background theme.
If you provide this option, default label will be replaced [string][default: None] axlabelfontsize Font size for axis labels [float][default: 9] axlabelfontname Font name for axis labels [string][default: 'Arial'] ylm Range of ticks to plot on Y-axis [float Tuple bottom, top, interval ][default: None] axtickfontsize Font size for axis ticks [float][default: 9] axtickfontname Font name for axis ticks [string][default: 'Arial'] yerrlw Error bar line width [float][default: None] yerrcw Error bar cap width [float][default: None] Returns: Bar-dot plot image in same directory bardot.
One sample : It should have atleast dependent res variable Two sample independent : It should have independent xfac and dependent res variables Two sample paired : It should have two dependent res variables xfac Independent group column name with two levels [string][default: None] res Dependent variable column name [string or list or Tuple ][default: None] evar t-test with equal variance [bool True or False ][default: True] alpha Significance level for confidence interval CI.
It should be one or two-dimensional contingency table. It must be non-negative and sum to 1. If you provide this option, default label will be replaced [string][default: None] axlabelfontsize Font size for axis labels [float][default: 9] axlabelfontname Font name for axis labels [string][default: 'Arial'] xlm Range of ticks to plot on X-axis [float Tuple bottom, top, interval ][default: None] ylm Range of ticks to plot on Y-axis [float Tuple bottom, top, interval ][default: None] axtickfontsize Font size for axis ticks [float][default: 9] axtickfontname Font name for axis ticks [string][default: 'Arial'] theme Change background theme.
It should not have missing data. The missing data will be omitted. It can be obtained from sklearn. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] figname name of figure [string ][default:'roc'] r Figure resolution in dpi [int][default: ].
If theme set to dark , the dark background will be produced instead of white [string][default:'None'] Returns: ROC plot image in same directory roc. Data should be in the format of ,,,,,, for 3-way venn and 2-way venn 10, 01, 11 [default: 1,1,1,1,1,1,1 ] venncolor Color Palette for Venn [color code][default: ' e', ' f', ' ffd' ] vennalpha Transparency of Venn [float 0 to 1 ][default: 0.
In my case, simple conversion seconds. Hi Greg, there was a lot of reflection is the past to decide what is the most optimal ;- so, at the. Dear All, first of all, Happy New Year to you all! Advise on selecting correct values to be analized. Hi Bianca, the situation with "paranoid" users and private networks is pretty common, and. Hi, I don't know if your manual editing of config files is correct or not, and so did you miss. Hi, I've analyzed little bit the code, and currently very curious how did you get such an error,.
It' work! How to keep custom Add-on in sync for 'long' running command. Host Name List only localhost. Hi Sushil, all is looking like your current database is "WAX", while your active.
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