# EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

## Documentation for package ‘Logolas’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

aRxiv | Counts of the aRxiv field categories of 4 UChicago Statistics professors. A dataset of compositional counts of 10 aRxiv field categories for 4 professors' publications in aRxiv.
EBF1_disc1 | EBF1_disc1 transcription factor position weight matrix A dataset of composition probabilities of A, C, G and T in 10 positions of the motif.
GetConsensusSeq | Function for obtaining consensus sequence of DNA sequence symbols from a PWM matrix
get_logo_heights | Get heights of logos in nlogomaker() under different scoring schemes
get_viewport_logo | Function for creating a multi-panel logo viewport
himalayan_fauna | Proportional abundances of different bird species in the Himalayan mountains A dataset of proportional composition of 140 bird species in 3 regions of the Himalayas.
histone_marks | Compositional data of histone marks in different regions of genome along with background information A list containing two matrices storing composition of 5 histone marks (H3K4ME1, H3K4ME2, H3K4ME3, H3AC, H4AC) in 5 regions of the genome
logomaker | Create logo plots from aligned sequences or positional frequency (weight) matrix
logo_pssm | Function to plot PSSM logo plot visualization.
makemylogo | Logo maker for a given English alphanumeric with common punctuations
mutation_sig | Compositional mutational signature data, with mismatch and flanking base frequencies reported A dataset of compositional weights for mismatches in the "0"the position (center of signature) and that of the bases A, C, G, T for two left flanking bases (-1, -2) and two right flanking bases (1, 2).
nlogomaker | Main workhorse function that builds negative logo plots
pssm | Position specific scoring matrix data A dataset of position specific sores of various amino acids in 9 positions binding domain.
seqlogo_example | An example of the position weight matrix taken from seqLogo package A dataset of composition probabilities of A, C, G and T in 8 positions of the motif.
UMI | An example of the position weight matrix of the bases in the first 30 positions from ends of sequenced reads (together with the barcode) A dataset of composition probabilities of A, C, G and T in 30 positions from the 5' end of reads.